So, if the main six were in prison, what crimes would they have done to end up there?

6886866
Applejack would probably be in for assaulting Rarity

Twilight Sparkle: since she's one of the leaders now, she can just say she's innocent. or something
Rarity: murdering her lover
Applejack: moonshining and/or fucking with her brother *scnr*
Pinkie Pie: drug trafficking
Fluttershy: eco-terrorism
Rainbow Dash: speeding

6886866
Twilight's probably in for war crimes or some shit, like banned inhuman experimentation on people and the such, maybe she invented pony poison gas at some point? I don't know.

6886877
This is before she became a ruler.

That's easy: Mass-murder.

Pinkie made a bunch of clones of herself. Being only a few days old: They caused a bunch of trouble, because they didn't know any better. Twilight's response was to kill them all, and her friends helped her do it.

6886979

Well, then for Twilight it's highly dangerous experimentation with dark magic.

Fluttershy stole animals: https://derpibooru.org/search?q=fluttershy+steals+animals