My biggest one was the MZ crashing every time I wanted to change an icon lol
But in all seriousness I'd love to know what people had the most trouble with. For me it was polishing the game. I know it's still very far from that ideal product that I had in my head. Overall I'm very satisfied with the end result but only can feel like there's still so much more to do but my lack in technical skill couldn't let me achieve it. I'm happy I got what I did so far without big plugins, the only one I used is a small one to skip the FIGH/ESCAPE menu in fights.
If you want you can check out my game here. Thanks if you do!