"I can't believe that she did this to you" is most likely the sentence you are looking for. It suggests she did one bad thing. It would be possible to say something like "I can't believe that she had done this to you twice before" if there is a repeating action of some kind, but the sentence would need to include some extra description, like I added.

The first is correct. "I can't believe that she did this to you" (or, depending on the context, "I can't believe that she did that to you".) In colloquial, everyday speech, most American English speakers would drop "that" and just say "I can't believe she did this [that] to you."