@1: Does this misalignment apply to all or some arenas? if for some (i fixed one misaligned arena yesterdey in my version), could you please find out which ones it applies to? There is an according message in the output_log.txt file, that would help to fix those affected
@2: Thats ... interesting. And bad. I'll look into it
@3: Depends on the weapon. Magical is not automatically unbreakable, especially if the magical weapon was "only" blessed by some god - magical alone just means "can damage demons". What *can* happen is that you lose the weapon in combat (yellow instead of red icon), this can happen to any weapon, and you should find it in the loot after a successful battle.