No, not the Sith, but the elements of the galaxy that are on the wrong side of the law; the elements that make the galaxy a bit less peaceful even in the relative safety and security of heart of Concord Space: organized crime, religious fanaticism, bigotry, and substance abuse to name a few. The Concord Navy and the various member security/military forces can't cover all of space at once, and there is a lot of space to cover; plenty of room for enterprising outlaws to slip through and make a quick load of credits. This post is going to detail some of the dangers that can lurk anywhere. These are threats to the Concord that aren't the obviously seen threats like the Romulan/Klingon Alliance, the Illithids, or the Nano-Terrors.
Organized Crime: From pirates to slavers to armed gangs, organized crime is alive and well in the far future. Where a species has a vice, something that is denied them by law, there is a group there willing to take the risk to get what is prohibited in the hands of those willing to risk the law to get it. Even on the most peaceful, law-abiding worlds, there is that element of users and pushers.
Hutt Syndicate: When Earth was going through Prohibition, which threw gasoline onto the fire of groups like Itallian and Irish Mobs, the Hutts had long perfected the arts of intimidation, racketeering, and slavery. Today, the Hutts are an example to criminal groups all over the galaxy what is possible, and an example to law enforcement groups of what they are striving to prevent. The Hutt Syndicate is a galactic power in their own right, with just as much political clout as any stellar nation.
The Hutts started off as trickster on the galactic stage. Their world, Varl, was dying, largely to the Hutts' total disregard for environmental protection due to their species being one that desires more of everything. To Hutts, he who dies with the most money, goods, slaves, etc. wins, and only those with more are worth anything at all. The Cataclysm of Varl forced the various Hutt cartels to work together to save their species. In a nearby system, they found what they needed: a world suitable for life and inhabited by "lesser" creatures that can either be easily eliminated or put to work. The Evocii of Evocar didn't stand a chance. They were a primitive people, only developed into their Bronze Age, who were awed by the Hutts and their technological wonders. They traded their lands for tech bit by bit until the Hutts ruled the whole of the planet. The Evocii were moved offworld to the moon Shadda to begin the development of spaceports, and Evocar was renamed Hutta. The enslavement of the Evocii elevated formerly subservient Hutts to a better class of being (after all, if Hutts are superior, then no Hutt should be on the level of slaves), even though those former slave-caste Hutts were still kept in their lower status by the ruling cartels. It also showed the Hutts just how easy it can be to buy an entire culture.
The Hutts spread throughout the nearby sectors, which are now known as Huttspace. They enslaved various species, forcing them into servitude at first by trickery like they did the Evocii, but then at gunpoint as more of the enslaved saw use as soldiers. Those that fought the Hutts had to deal with their oftentimes technological superiority, and then the ferocity of their troops. Species like the Nikto, Barada, Klatoonians, Weequay, quickly fell to the Hutts and make up the majority of their "army." Other cultures, too strong to bother with subjugation, were subverted by the Hutts who have a knack for finding a person's vice and exploiting it. They also formed criminal alliances with various slavers, like the notorious Gnolls, and gun-runners and smugglers to expand their influence to the point that few places in the civilized galaxy are free of the taint of illict activities that are somehow under Hutt control.
Politically, the Hutts deny any wrong-doing. The dealings with the Evocii, while unscrupulous on the surface, were all legally biding. After all, it's not their fault that the Evocii didn't truly know the value of their own land...or any of the other primitives that they swindled in a similar matter. The Council of Houses, which is the public face of the Hutt Syndicate (the Hutts refer to their worlds as an Empire), denies any of the exposed criminal activity as the work of rogue houses, and not the official actions of the Hutt Empire. They are not members of the Concord, but they do have dealings with many Concord members that neighbor Huttspace (something that causes great concern among many Concord members who worry about Hutt influence on those nations in Senate matters). It's hard not to. They are a major force in that area of the galaxy. The Concord (any everyone else for that matter) is powerless to affect Hutt operations without risking all-out war, so they focus on tracking down and arresting criminal agents of the Hutts in Concord space wherever they can be found.
Slavery: Slavery is not just a human problem, but one that exists throughout the galaxy. Slaves are taken for a variety of reasons ranging from labor to prostitution to even taking slaves to breed as a food source for other sentients. Slavery also takes many forms from indentured servitude where the slave is largely treated as an employee, to caste systems that keep the lowest castes as servants and/or playthings, to slavery in the traditional sense with all the abuses and horrors that go along with it. While most civilized species outlaw such practices, there are still many that profit from the buying and selling of sentient beings like livestock. The Hutts, Drow, Gnolls, Neogi, Medurr, Aboleth, Gravs, Illithids, and countless criminal organizations still utilize the practice. Even some corporations have had their "hiring" practices called into question. Most notably, Voidcorp's "accquisition" of Sheya and the inhabitants, the Sesheyans, is very reminiscient of how the Hutts enslaved the Evocii.
The plight of slaves varies wildly. Some are well-cared for and afforded many freedoms and even do not mind their status as slaves, while others are beaten, tortured, and forced to perform disgusting acts for their masters. There are entire colonies of people that are either freed or escaped slaves huddling together for protection, fearing every outsider, and dreading every unknown starship that shows up on their sensors. To these poor souls, even though they have regained their freedom, they are never truly free.
Narcotics: Sadly, one of the common traits among many species beyond the humanoid form is the need or desire to get "high." The galaxy offers a dizzyingly array of ways to become intoxicated from drinks and inhalants, to injections and ointments. What is a common spice to one species can be an addictive substance to another, like common table salt. (The Arcona recieve a strong hallucinogenic effect from the same salt that humans and other species use to season their food.) When a new species is encountered, there are groups that race to find out what that species' vice is, so they can exploit it. The more technologically advanced the species, the bigger the goldrush. Some drugs only affect certain species, and then there are drugs that only affect psions.
Drug abuse is a constant problem on most worlds. Even though the use of many substances is legal, though by and large controlled, abuse and all the evils that come with it from theft to murder to slavery still keeps many law enforcement agencies very busy. Add in that narcotics that can be legally acquired are often times weaker than those purchased from drug dealers doing business in dark passageways and crowded bars, and smuggling is another wrinkle to iron out.
It would be impossible to give a full listing of all of the narcotics, their effects, and who they affect. Common human drugs like tobacco, marijuana, cocaine, and heroin can still be found alongside new drugs like Jub-jub, Red Sand, Stardust, and Blood Jelly, just to name a few. Those that sell these drugs can be found all over from spaceports to cantinas to even the mess halls of Concord capital ships. There is big money to be made selling and smuggling narcotics, and even otherwise law-abiding merchant vessels will offer goods that are inocuous to most species, but highly addictive to some species along their trade route.
Bigotry: Another sad common thread between many species is bigotry. Whether its garden variety racism or "specieism", hatred based on moral ground, or simple xenophobia, hate isn't hard to find. While bigotry is held in very low regard in the court of popular opinion in most cultures, and making politcal and business decisions are outlawed by the Concord in inter-culture dealings and among most member cultures, it still occurs with little to no recourse to take by the victim. Even today, with as long as humans, fraal, and moreau have shared a close-knit culture, bigotry is still a part of life in many parts of the Sol Alliance systems. While words are the common weapon weidled by bigots, too many times conventional weaponry is used to do the damage that words cannnot.
Humans recieve a lot of blame for being bigots, but they are far from the only species. Some Turians still harbor feelings of hatred towards humans, and see them as savages or arrogant primitives with too much influence in the Concord. Cardassians (primarily religious and political/military leaders) see themselves as the pinnacle of humanoid evolution, and see all other species as beings just waiting to be conquered. Salarians still harbor feelings of distrust towards Krogan, seeing them as primitives who are only what they are because of Salarian "uplifting" of their species.
Below are a couple of examples of groups that are prime examples of bigotry fueling a dangerous terrorist agenda.
Cerberus: Cerberus is a large "pro-human" group. Due to attacks on various installations where aliens gather in human space, even going so far as attacking the Kreskin Academy. They got their start not long after first contact with the Fraal. In those early days, they weren't much different than other racist groups in Earth's history, but as the wave of anti-alien and then anti-psion hysteria began to gain steam, the group started to receive large influxes of cash that they used to arm themselves with the best weapons and armor they could acquire. Even then, it wasn't until the organization was lead by a mysterious figure known as The Illusive Man that Cerberus became a serious threat to human-alien relations, and even to the stability of the Concord as a whole.
No longer is psionics or cybernetics focii for their hatred. They are not concerned with "human purity" (although mutants are not welcome amongst their ranks) and are willing to use all the tools at humanity's disposal from psionics to genetic engineering to attain their current goal: human survival and dominance at any cost. They will even work with other species if the end result furthers their goals, though finding members of other species that know of Cerberus and still willing to work with them is rare indeed. They are not just simply a terrorist organization under the Illusive Man's rule, but an economic and political force of nature. Cerberus controls several corporations through stocks, and use the research and resources of those corps to further their goals. It is feared that Cerberus has many operatives in the Sol Alliance government and in the Alliance's Concord represenatives' offices in the Concord. There have been connections uncovered of Cerberus influence on politicians in the past, mostly through blackmail, but Sol Alliance Intelligence thinks the links may go far deeper today.
The Sword of God: When it was finally confirmed that humanity was not alone in the universe, many religions found themselves with questions about the existence, or at least the far-reaching power of their deities. Many were able to weather the questions and evolve their doctrines to include aliens into their dogma either by reinterpretation of their scriptures or the integrations of similar alien religions under their dogmatic umbrella. Others were aghast to find that among the multitude of species in the galaxy none shared their belief. This proved to some that their religion was a farce all along, while others became convinced that this was a sign to take their faith into the galaxy and bring aliens into the ranks of the true believers. Still, there were those that saw aliens as nothing more than demons and temptors to pull the righteous away from their god. Some of these groups used violence to lash out and hopefully drive away alien influences from god's chosen species. Most of these groups died out with the passage of time...and a healthy application of arrests and incarceration. One that did not, however, was The Sword of God.
The Sword of God is a largely Christian group, though they will accept any human who follows one of the three Abrahamic religions (inter-religion violence and bigotry largely died out in the late 21st century), and have even counted other faiths like Hindus, Wiccans, and so forth among their ranks, albeit these were very rare. They formed in the early days of the Illithid Invasion. Their members are typically hard-line fanatics that see humans as the only true species and that all others are nothing more than tricksters and demons luring humanity away from the one true God, who should therefore be purged from human society. They have been credited with several attacks on fraal on Earth, and the 2347 bombing of an Ithorian worldship docked at the Severain Shipyards in the Corliss system.
Their current leader is a named known as Reverend Ernesto Gulogovich. It is unlikely that is his real name, however, as he is wanted throughout much of Concord space for various terrorist acts. The Sword of God uses subterfuge to get their operatives into positions where they can cause the most harm, and gain the largest kill count. Where Cerberus largely uses their might to influence human society behind the scenes, The Sword of God is all about cutting a bloody swath through aliens, and humans that live closely among aliens. They love to target alien places of worship and human religious institutions that accept alien followers. Their most public attack was that on a large church on Earth, an evangelical Christian church that had just appointed their first alien, a fraal, as a church elder. During Sunday service, the Sword rolled up in armored trucks, stormed into the service an opened fire. When emergency crews appeared on the scene, another firefight erupted that took the police unawares since they expected a hostage crisis. The Sword members were not interested in taking hostages, however, and attempted to kill their way through the police barracades. Their actions were televised live over the Grid for all to see. Over 600 innocent people lost their lives in that attack, including 38 police officers. All 20 Sword members were slain.
The Sword of God is a difficult group to pin down. Their numbers are not known, though Rev. Gulogovich claims their ranks are in the hundreds of thousands. They tend to be mobile and keep their presence in an area secret until time to strike. Most of their operations are not suicide missions like the massacre on Earth. They feel that God wants their followers to live to carry on their work, but if one should fall int ehir holy quest they will be welcomed into the afterlife as a hero. The most that have been captured at any one time have been 50 members in an unregistered colony on Mars. Usually, if 3-5 members are captured at any one time, it is considered a great coup.