That's... odd. You keep running into your counter team. Survival run seems fine on my end however. A healthy mix of all 5 classes with different line-ups, not just the one that counters mine.
You are right on the AI's lineups not always matching the actual lineup of the (other) players. This happens to me rarely however.
As or that pesky Hinata, just throw her boyfriend Naruto in front of her. Problem solved!