Like reprep said, the issue appears to be a coincidence. But if you're emulating with goomba, there is zero risk, even if such a bug does exist.
Yeah, I'm sure it won't replicate that exact thing.
It seems to be working nicely, the only problem I have is that sometimes it glitches out and breaks the game, I then have to open the menu on goomba and select "exit" which doesn't actually exit but restarts Goomba/the entire GBA ROM all over.
I don't know if it's Goomba Color's fault or my M3 glitching out and reading my SD wrong, though that shouldn't be the case since it doesn't read the ROM from the SD card but the RAM on my M3.
I haven't seen the problem happen in versions of Goomba that aren't in color. I'm hoping it's just Goomba Color's fault (no offense to DWedit, you can fix a bug, but you can't fix a broken flashcart.)