A few planets or systems are corrupt off the charts, but unless they do something heinous they get away with it. Officially. In reality, the Alliance Troubleshooters exist specifically to deal with threats to the Alliance that official channels have trouble with. More than a few would-be genocidal dictators have disappeared after ignoring warnings from the Council.
One unaffiliated planet is a Libertarian’s dream — the government is officially a federated republic, but acts as a de facto theocracy more interested in oppressing minorities and women than actually running the state. They have almost no laws, no public services (including schools, medicine, or even infrastructure; these are all built and maintained by private interests, with varying degrees of success), no equal rights except for the rich members of the in-group (the right race, sex, political leanings and religion), or news that isn’t propaganda. Their government is considered the most corrupt in Alliance space; bribery is openly considered a standard political tool, and outsiders who know what it’s like down there consider even Void Pirates to be more honorable. Local IQ is a full standard deviation or two below that of Alliance humans in general, and people approaching normal intelligence or (Elvis forbid) higher are either crushed by the herds of ignorami, rise to positions of power and further the corruption, or escape. They’re also paranoid beyond words, living in perpetual fear of The Enemy (which seems to change weekly) invading or bombarding them into oblivion from orbit. That their “news” is full of such stories (with little or no basis in reality) is surely a coincidence. As a result, the population is armed to the teeth. Their local tech is a good several decades behind the Alliance baseline but they have cutting-edge weapons tech, almost all either imported or flagrantly copied from imports — which is perfectly legal since offworld corporations have no legal standing there. The Patrol maintains a small interdiction force to prevent their periodic invasion fleets from attacking Alliance worlds — they launch one every few years after some demagogue whips the less-intelligent members of the population into a frenzy against the enemy du jour. These invasions always follow the same pattern: ship or ships are launched, the Patrol tells them to stand down, they fire on the Patrol, and the Patrol obliterates them. While this doesn’t help the Alliance’s reputation among the people down there, Patrol command doesn’t care. They were written off as a lost cause decades ago, and orbital bombardment on civilians is just gauche. Every analyst in the Patrol has come to the conclusion that the planet is essentially immune to invasion thanks to the population’s ridiculous level of personal armament. Their hidebound fanaticism also renders them immune to reason if it conflicts with their existing way of life, even if demonstrated beyond any doubt by a civilized human being. Oddly enough, the planet also suffers repeated attacks by Void Pirates who seem to slip past the Patrol with alarming frequency. Considering the Patrol exists in large part to destroy pirates, wild theories of collusion between Patrol and Pirate forces are dismissed out of hand.
There’s a Lost Colony settled by First Nations people from Earth out there at the edge of the galaxy. Nanabozho – named after their trickster god – wasn’t inhabitable when they got there, but it wasn’t actively hostile. They have since partially terraformed it and built vast domes to house herds of transplanted wildlife. Their plan all along had been to populate Tau Ceti with North American lifeforms, so they had extensive gene banks and facilities. With their sudden unplanned independence from the rest of the fleet, they ran with it and created a tribal society. Their end result is a fascinating amalgam of First Nations Great Plains and Eastern Woodlands society with infinitely higher technology than they had had before North America was colonized. The people of Nanabozho will likely decline Alliance membership if it’s offered for obvious reasons.
Another unaffiliated planet has been locked in a bloody war of genocide between its two remaining nations. Both sides’ societies have been destroyed by the decades of war and now exist solely as military juntas dedicated to preserving “our way of life.” This is despite said ways of life being nearly identical and barely remembered by even the oldest survivors, who were themselves only told about it by their parents or grandparents. Both sides are desperate enough to use extreme measures; chemical, biological, and nuclear weapons have been used by both sides, and they would happily use even worse if they discovered it. Rumors of genetically-engineered supersoldiers using cutting-edge bionics and war machines have begun to circulate. Most of these rumors are ignored, as the decades of war have reduced most of the local manufacturing and scientific capabilities to the equivalent of WWII. If anyone ventured down to the surface, they would see an eclectic mix of relatively modern (if old and worn) Alliance technology mixed with equipment on par with an MP5 or AK-47, and some soldiers walking around with even more primitive gear. The Patrol, naturally, maintains a blockade, but it isn’t very active. So far the locals have been content to kill each other rather than look up.
Corrado is a case study in “it isn’t illegal for some people, but the rest of y’all are screwed.” It maintains trade links to the Alliance, but that’s about it. The planet was a wildcat colony settled by a group of miners looking to make the next killing in whatever they could dig up, since then it’s grown into a family-run corporation much more closely resembling a Mafia than General Electric. And their plan worked – the planet is indeed mineral rich and inhabitable, with at least one lesser body that’s even more rich in minerals. That the lesser world is almost uninhabitable and toxic to human life was just a minor concern. Never one to pass up an opportunity, they started importing “guest labor.” This more closely resembled how Al Swearngen “recruited” the staff for his saloons than anything resembling reputable employment. That there is no extradition with the Alliance and the Patrol is not welcome there backed up by Patrol regulations and jurisdictions is just a coincidence. It also is just a coincidence that anti-government demonstrators tend to go missing with alarming frequency, and rumors abound of prisoners being sentenced to spend the rest of their lives mining with the bare minimum safety gear necessary for bare survival on the mining colony.
These are just four examples of what goes on outside of Alliance oversight.