It wasn't like they just guessed or anything. IIRC they had a test where people coughed into a petri dish with and without masks. The initial results showed that there was coronavirus on the outside of the mask, leading them to conclude that the virus is able to get through the mask. They weren't able to realize they were incorrect on their conclusion until they looked at the cultures a few weeks later and measure the amount of coronavirus in them.

I could be wrong on that, if someone is better-informed please correct me, but that's what I read somewhere.

EDIT: Just to clarify before I'm downvoted, I do actually agree they were a bit too hasty to tell people not to buy masks. Having the surgeon general tweet out saying "Seriously people, DO NOT BUY MASKS" was definitely premature and obviously led to a lot of the problems we're having here now. I just wanted to point out that it wasn't a completely unfounded take, just premature to make huge decisions like that.