So I don't know if anyone else ran into this glitch. Figured I'd mention it just in case.
Don't know if it's a glitch limited only to when you have a 2nd player playing, if it's limited to the Wii U, or if it's limited to Wii U having a 2nd player playing. Anywho... me and my sister had just started the Avengers Assemble mission. I was the primary player as Thor, she was Widow in the Quinjet circling Stark Tower. The glitch happened when I (as Thor) got Loki down onto the main landing platform. She, in the Quinjet, got hit and exploded and the problem came that every time the jet respawned she immediately exploded again. The trick comes when it forces our places to switch (so me, as the primary player, takes over the Quinjet) to destroy the 10 Chitauri vessels/sleds around the tower. Difficult to do when spontaneously exploding. I managed to destroy like 3 by sheer luck/getting off a shot or two before exploding.
The workaround seemed to simply be to restart the mission as a single player only (have player 2 avoid jumping in/joining the game until after you've defeated Loki on the tower).
Like I said, just thought I would throw this out there in case anyone else came across it.