Most of the issues the game currently has have been there for quite some time. You don't even need rocks to bypass the fence, simply walking into the fence while switching to overhead view lets you cross it with no issue so long as the camera is in the same position in both "player" mode and "god" mode. I've never had any characters bug out from combat but eventually you get slimes that allow you to make healing potions, you could try to heal them but beyond that, and if restarting doesn't fix it, I don't know what else to say other than it sounds like a pretty bad bug. The dev has supposedly fixed some pathfinding problems in the latest update that we haven't gotten (here) yet so ideally that would have fixed the issue of the characters getting stuck and requiring restart to temporarily fix them.
Animations have always had problems, from clipping, sync issues, unfinished pairings, misalignment, and as you've seen first hand they sometimes initiate a paired animation alone.