Hey! Thanks a lot for updating this wonderful hack :)
2 problems I've found so far- the Aqua Team guy that gives Tyrogue egg does that multiple times- for me, he was there twice and gave me the Tyrogue egg twice (hatched them and confirmed it's 2 level 5 Tyrogues).
Another small thing- when I got to the family house where you fight 4 trainers above Mauville, they were in the house and had the dialogue they have AFTER you beat them, including the Macho Brace, but I didn't get the chance to fight them.
EDIT: I'll edit this as I go-
after you go up from Mauville, near the mountain entrance there is a girl but you cannot interact with her- also, curiously, there is a wailmer-like object stuck in the mountain, looks like a glitch.
Combusken learns Fire Punch before turning into Blaziken, then Blaziken learns Blaze Kick, then at level 38 Blaziken learns the inferior Fire Punch.
The upper right stone in Lavaridge is not interact-able.