This is a bad headline and it implies more than is actually documented by the journalist. Let's take a look at the true meaning of the word "refute":

https://en.wiktionary.org/wiki/refute

"Refute" means "To prove something to be false or incorrect."

This headline is abusing a proscribed meaning of "refute": "To deny the truth or correctness of something."

Cruise has offered no evidence but only a press release in which they make counterclaims. To be fair, SFFD didn't really provide any evidence in their claims, either. So this is simply "he said, she said" until there is concrete sensor evidence to the contrary.