I think that, grammatically, the subject of the Czech sentence might be ty, going along with the second-person-singular verb. So I can understand why ion1122 would suggest "were you it" as a translation. However, that seems a little strange, outside the context of a game of "tag," and "Was it you" works much better on the English side.
I don't speak Czech (why else would I be here?) but the subject of the English sentence: Was it you? is, clearly, IT, which is why it requires "was" and not "were". I wish I could understand what the Czech sentence really means...