It's a known problem. It's due to the fact that the hackers, that made Brown, re-programmed the sprite-loading routine, however, they probably didn't take into account one thing: VRAM (i.e. the gbc hardware area where graphics are loaded) is not accessible all the time (it has a cycle: inaccessible for 59 milliseconds, then accessible for 1.1 millisecond, then again inaccessible for 59 milliseconds, and so on).
So they probably only tested their new code on VBA, which is well known for not emulating the real GB's VRAM inaccessibility, so if you play it on an actual gbc it will show the flaw. If you try to play Brown on BGB, it has a checkbox option where you can choose wheter emulate the VRAM inaccessibility or not. The two results would be the following:
[VRAM inaccessible]
[VRAM accessible]
Also, creators of Brown don't seem to care about correcting this issue so you just have to play it with that problem (if you're using a real GB) or play it on an emulator that doesn't care for VRAM accessibility.