Yes, but when you plan a game scenario, you don't write it chronologically, so it's not like the first point they said her name they decided you wouldn't get to rename her. If that were the case, after they'd made that decision, they would have logically go back to those areas of the script that no longer make sense. That's why I agree with Vyk on the editing issue.
All of this makes me think Wakka did it. He be like: "Hey, village, listen up, ya? There's this new guy here and I thought it would be a good idea to troll him into not knowing Yuna's a girl. Of course, after he finds out, you can go back to talking about her normally. It's gonna be so much fun, ya?"