The same thing happened with me, but using SLKR's team. Two battles in a row when there was only Dark Trooper and Scout Trooper left. SKLR did his ultimate, and then shortly after all the controls disappear. I can still turn auto on/off, but the characters don't fight. I can also select both of the enemy troopers, but can't do anything to hurt them.
I have similar data disks. BLUE: volatile accelerator, amplify agony, protection shield, thermal exhaust, GREEN: defensive formation II, ability exhaust
Once the timer runs out, it just stays there until I choose to forfeit.