Only 2 bugs so far. (Amazingly enough,) the ROM corrupted only once since I started coding it, and I'm pretty sure it was because I copy-pasted some commands. I never copy-paste anything now. Maybe it wasn't even corruption, but a black frozen screen in any case.
I think the problem with CE is not that we corrupt things, but that there was already a corrupted thingy lurking in the 2-year-old ROM and we just couldn't get rid of it even with exports. Anyway, I make tons of backups for Prophet's Guile and I simply restored the good ROM, so there's no problem.
As for the bugs:
Magus Castle
When the portal opens, Crono's party is "teleported" to the center of the screen and Magus to the top-right corner of the screen. I checked the commands and it seems that for some reason, it's due to the fact that there's no battle. If there's a battle, the characters will be correctly placed when the mode-7 portal opens. If there's no battle, they get displaced. I don't think there's a solution to this bug since we can't really have a Magus vs. party battle (or can we? ...no, probably too much bothersome to hack).
Skyways
In every Skyway overworld sequence, 3 characters are shown instead of just Magus (Frog and Marle I think). We probably just have to delete some commands in the Overworld Events, but I don't know which.
If anyone has some solutions for those bugs, you know what to do...