Except Tifa is confused because she know that most details of the story Cloud was telling were accurate except for the weird detail that the SOLDIER member who came with Sephiroth wasn't Cloud. It's still pretty odd that she wouldn't say anything, but don't act like she knew exactly what was going on. She doesn't know why Cloud knows what happened but is inserting himself into someone else's role. Yes, obviously they have her keep quiet so they can make the big reveal later, but her silence isn't entirely unreasonable. Maybe she's doubting her own memory somewhat or doesn't want to challenge Cloud on it because it doesn't seem like that big a deal to her at the time. It's only later on when Sephiroth suggests this means he's not the real Cloud at all that the inconsistency seems to take on greater importance.