so this patch should fix most of your problems
Thank you for your work!
A couple more bugs I found after my message yesterday; 1) Mermaid Misty sprite not showing in the diving section of the quest. It was only my character underwater. 2) The open manhole in the middle of Celadon leads to the restaurant that is southeast of the map. 3)Picking up any pokeball in route 777 leads to an error that reads "Script'Interpreter' line 188: EventScriptError occured". Also the new ace trainers there are strangely larger than the standard npcs. 4) All the team aqua grunts are still there at the beach even after Melanie's sidequest.
Mermaid Misty won't appear for me (as shown in the pic above) in 5.39, idk if this is now fixed in 5.40 since I encountered a new bug. Upon opening the game, it crashes immediately, showing an error message that read "Script '<internal:marshal>' line 34: ArgumentError occured. Undefined class/module Player::Instant Messages". I tried re-extracting itand redownloading it but it still showed up.
I can't re-enter Rest House 4 here, but after the quest ends and the safari zone is back to normal, I can re-enter it normally, at the cost of not being able to go to the abandoned lab from here. You can't also approach the middle section of the abandoned lab, even after the safari zone is safe.
This whole cutscene repeats when you fly out towards Celadon and re-enter through the previous building. (This is before finishing the Sarah questline.)
After turning Oakley into a bunny girl and re-entering the room, Oakley becomes bunny Annie and actual Annie returns to her normal sprite even though she was also a bunny girl. Annie's induction is also unskippable unlike Oakley's, and contains GF's induction instead. Also, unlike GF and Mela, turning them into bunny girls won't make them appear in the casino. Speaking of which, if you turn Erika "nude" then select "casual" after, it will say that she's in her casual clothes, even though her mugshot and overworld sprite are naked.