The scene when you reach the first Rin Travel Agency. Where Tidus is talking to Yuna about Sin and the Calm.

I can't remember it exactly, but it was something like:

"What was it we did that was so bad? ...Oh, was it using lots of machina or something like that? Oh. ...Wait, was that really so bad?"

It just felt wrong. The tone and dialogue don't match up. In that one bit, he shifts through three different states. From cluelessness, to understanding that it was the machina, to questioning it. It happened way too fast to feel natural. If it had happened that fast, the reaction wouldn't have been bemused questioning, it would have been a lot more serious and intense, closer to Wakka's reaction on the S.S.Liki. "What, you mean Sin's killing everyone for something that happened a thousand years ago?! Are you sure?" That scene just never really felt right to me. Although it is all a writing and directing issue, not a voice acting one.