Any time I do a puzzle in Nightfall Bandit Dungeon (the only one I've tried so far) and get into a battle with one of the 4 star pets, or a 5 star avatar, my 3 pet's mana goes to 0, this makes it impossible to do finishing blows on them with the mana I've earned from previous battles.

I haven't been playing for a while, and just came back, I don't know if this was intentional, but it wasn't like this before, so I assume this is new.

Yep. Dungeon bosses will clear buffs and purge mana before engaging them.