Players in Orchestra are typically employed by shadowy agents or faction officers, so odds are that during their adventures they will step on a few toes, whether it's the people with legal jurisdiction in the area or a group of organized criminals.
The general rule is that once you get into trouble with a more traditional faction, you don't get out. The World League's prisons for violent criminals or subversive elements are incredibly bad, the Swordsman Foundation can't risk someone being a bad apple. Similarly, if you get in trouble in an independent town in the Cataclysm Zone, you probably won't be invited back. Organized crime actually functions a lot like one of these traditional governments, they will never overlook a transgression without a fair amount of repayment (which is where they differ, since they never look at jail time or expulsion).
The World League has an “Infraction” system they use to grade crimes on a scale of 1 to 12. A Class 1 or 2 Infraction typically only carries a hefty fine, though frequent offenders may look at imprisonment. Police will not typically stop someone for a Class 1 or 2 Infraction unless they're a persona non grata, but they will tack them on to higher class Infractions. Class 3 or 4 Infractions committed in plain sight of a police officer will cause them to stop the individual, and can occasionally include prison time. Suspicion of a Class 5 or 6 Infraction will lead to a stop, while even rumors of having committed a Class 7 or 8 Infraction are sufficient to bring someone in for questioning. A Class 9 or 10 Infraction is enough to start a manhunt, and Class 11 and 12 Infractions lead to roadblocks and lockdowns, as the police go into overdrive looking for the criminal.
Of course, World League law enforcement is anything but uniform- bribed officials may sell weapon permits (up to Class 9) (or “licenses to kill”, though savvy law enforcement officers not that the maximum crime waiver is Class 6, and will see through any license above that).
Corporations and anarchists, however, are more forgiving as a rule. Since corporations care about their bottom line, if they think you're willing to help them or hurt their enemies, they'll let a certain amount of misdeeds slide (though they'll still confiscate your guns). Anarchists don't necessarily forgive the transgressions of others, but it is possible to win back their favor (most anarchic communities have a reputation system that keeps track of who benefits the community, who's a deadbeat, and who's a marauding bandit). Similarly, some anarchists don't care what you've done to other anarchists, so long as you're not hostile to them as a whole.
If you're in World League territory and you step on someone's toes, you have an advantage and a disadvantage. You're one of probably at least a thousand people that someone would see in a day if they were strolling around, so you have a lesser chance of being found by an individual hunter (all bets are off if you're on a wanted poster). The downside is that there's a lot of paper trails, and even organized crime's got people who can track them down. You'll end up paying more for your lifestyle, and it may have a negative impact in some Scenes.
In the Cataclysm Zone people are typically more forgiving, since it's a struggle to live day to day most minor things will be ignored. So long as you don't kill or injure anyone (or steal anything that someone needs, including food), you'll only get expelled from an area at worst. Of course, should you come back from exile or commit a heinous crime, you're likely to get a good old fashioned electric chair.