OK! I'm back! I was going to put my findings into a database, but it just didn't seem worth it as there were so few.
Here they are (with repeats):
1. (Repeated) The two characters who use the phrase (one once, the other twice) "planetary bioscience". It sounded stilted and unnatural when I was playing. It was funny when the blue collar guy said it, but the woman inside (if I'm remembering correctly) saying it twice seemed odd. It'd be cool if there was another way of phrasing it for her.
2. (Repeated) I still think "What are you going to do about this grief?!" is uncharacteristically clunky, especially given the situation that Cloud is reacting to. He (and everyone else) would have been in shock. A more natural response might be "What are you going to do about all this pain you've caused?!". (See here for another change you said you liked, too: http://forums.qhimm.com/index.php?topic=14914.msg248701#msg248701
3. The Icicle Inn is renamed to Icicle Lodge... but you can see a sign that says "Inn" in the game. Technically I guess that Lodge might refer to the whole area. Anyways, I'm just mentioning it, you don't need to comment on it.
4. This is a genuine bug: Red XIII's dialogue on the Highwind after defeating Hojo is broken or missing. There are a few instances where this happens.
5. I don't know why the Black Chocobo has been named "Invincible"? I thought he was literally going to be unbeatable, but I beat him several times during my playthrough. (Explained below.)Edit:
6. Forgot to mention this one: Bahamut Zero is totally messed up and doesn't play correctly. (In the DB already.)
7. Despite the 60fps, there was lots of very jittery animation, and it wasn't slight. (I know this is mentioned in the DB, but the DB makes it sound more minor than I found it to be.)
8. I also saw lots of graphical corruption thanks to the transparent menu in battles. (Again, it's mentioned already, but I saw a lot of it.) Kind of wished the menu wasn't transparent after a while :-/
And, er, that's it! Not so many things really. (The only time I noticed poor placement of the dialogue boxes was during the flashback on the back of truck with Cloud and Zax.)
I didn't play with Beacause for the first chunk of the game, so it's possible there's more in the first half.
I hope this is somewhat helpful. Apologies if the Red XIII dialogue is already in the bug DB.