I've originally planned this fangame to support all Gameboy models until I've realized that its poor performance on both DMG and Super Gameboy models wouldn't be an enjoyable experience, so I've added a lock-out screen & Super Gameboy border to highlight the fact. Since some emulators allow Super Gameboy borders to be displayed while playing in GBC mode, I believe that's where the issue is coming from.
A true fix for this is to either port the fangame to GB Studio 4 where the ROM can truly be set in "color only", or remove the Super Gameboy border altogether. (Editing the ROM's code may also work, though I'm not sure how as it's built from GB Studio's own ROM exporting option.)
Maybe I'll make a somewhat updated version of this fangame that fixes this issue, but that'll be for another day. Thanks for the help though!