Question: How did Hugo Strange find out that Bruce is really Batman?
Answer: Listen to the fourth Riddler interview tape. He did a psychological profile of Batman, then picked among candidates as to who could be Batman. He's also smart enough to realize only a rich man could afford all of Batman's gear and vehicles.
Revealing mistake: When Clayface disguised as Joker is holding Talia hostage in the movie theater, they are both standing on stage in front of the screen with a movie playing. However, they are not casting shadows on the screen. Also, no shadow appears on the screen when Clayface takes on his true form.
Batman: It was all a lie. There's nothing wrong with you.
Joker: Nice of you to say. But you of all people should know there's plenty wrong with me.
Trivia: Just before Protocol 10 starts, you end up in a giant fight with Joker and a good number of his goons. If you activate Detective Vision during this fight, you'll see that Joker doesn't have a skeleton. This is also true when he's holding Talia hostage in front of the move theater. This offers a hint to how the plot plays out.
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Answer: Batman later in the game discovers that Hugo Strange has been supplying everybody with weapons, so he would have given Two-Face the vat of acid.