If I understand correctly, a Zone of Truth spell has verified that the PC's don't think they're guilty, but also verified the account of their accuser. Therefore, one of the two (accused/accuser) must be mistaken, though he/she/they truly believe what they're saying.
Possible responses by the party are:
1. Unless the pc's are in imminent danger of hanging or something equally severe, investigate and try to solve the crime.
2. Alternatively, if that isn't feasible, convince the accuser to drop the charges. There are, of course, honorable and not-so-honorable ways of accomplishing this.
3. Break them out of jail (or leave town). Lots of complications with this course, as the entire party becomes wanted by the authorities. Naturally, this is the option most groups I've gamed with would select (sigh...)
If you're asking the question as a GM (not a player), then how the authorities respond is critical. If the pc's are new in town, and their accuser is an upstanding citizen, guess who's likely to be believed? On the other hand, if the pc's have never caused trouble - maybe even helped out at times - the authorities would be far more likely to give them the opportunity to prove their innocence. Either way, I suggest leaving it up to the players what to do, but make sure they understand there will be consequences to their actions. Maybe they'll take the hint and not immediately attempt to use force to solve the problem. Sounds fun - unless the pc's end up getting hung, of course
