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I've run into a problem in free play where the computer will only select five members for my team in free play, leaving me three short. It will not select Robin or Harvey Dent (I'm going in order and have finished the first four stages of the first mission), so there are things I can't access. Is this typical, or does my game have a technical problem?
If this is in the first story, at the botanical gardens, try selecting Clayface as your primary, then the rest of the team should fill out properly.
I ran into something similar, when I selected Mr. Freeze. I wound up with less than a full team, and more than one Mr. Freeze. Also, Batman would turn into Mr. Freeze when he used the Demolition Suit changer.