Eek! Do you have a save game from before the fight, and if so is the bug repeatable?
Sounds like it’s worth sending a save with hostile Wyll & Zevlor and a save from before the battle to Larian to see if it can help them fix this. I can only guess that there’s something about the allegiance of the Entombed Scribe that’s setting them off, as it would have been an enemy, then they turn hostile to you as you’re its ally?
I haven’t played around with Control Undead so confess I don’t know how it works. Sounds cool apart from this rather significant problem! Hopefully you can reload and release the skeleton before the grove gate fight as a workaround?