Can you tell me your team, as it doesn't seem to be the Banshees. I just can't replicate it.
Unevolved (Level 40) Tio, Maria, Irina, Camila, Valerie, Braga.
I've continued to play and for what it's worth in narrowing down the bug, I've evolved Tio and Maria and the battles that were crashing before have had a modest reduction in that happening (but it hasn't stopped completely).
I've noted the auto-battle crash happening very consistently on the following stages: R-3, R-2, and 1-8.
Additionally (if this it at all helpful), on those stages when I was unevolved, if I defeated and removed the backline banshees I could usually get away with turning auto-battling back on for the remainder of the battle.