Not to mention Tifa knew the entire time and said nothing.
I think this was more of her knowing something wasn't right but because of parts of Cloud's story making sense, she wasn't sure what. Cloud reiterating Zack's memories lined up with hers and she was confused as to how he knew that, because he wasnt there (or so she thought). So yeah...she clammed up. Then they dug out HOW Cloud knew that, and it wasn't because of the illusion Sephiroth/Jenova showed them previously in that Nibelheim flashback.