If they successfully debunked it you could say they refuted it.

People sometimes use the same word to mean simply arguing against something (whether successfully or not) but I think the correct word in that case would be repudiate.

Also, to be picky, if something is a fact, it can't really be debunked. If it is genuinely debunked then it was never really a fact, even if people previously believed that it was.

Contrarian?

Skeptic?