Ive only ran into one real game breaking bug so far
Talking to this NPC softlocks the game
I get same issue when I first met Sesame in Dark Realm.
I find a way to "skip" this problem.
Do not patch through a program your jap rom. Just load jap rom with your mGBA (if you use another emulator, then, I suggest you save a gamesharksnapshot of your game.)
After that loading jap rom, load snapshot, load game, start a dialogue when this problem occurs, skip a bad replies by pressing "A" key. THEN SAVE STATE.
Then load bps patch thorugh "File -> Load Patch", and game will reset with patch applied. So, just load savestate that you used. Replies will be in jap, BUT DONT WORRY, just press "A" to skip jap replie, and VOILA! next reply will be at english!
Well, atleast this worked for me.
Now you can keep playing at mGBA or return to your previous emulator (vba for me) and\or patched rom, like myself.
And, you always can repeat this if you meet this problem again. And you can keep playing.
PS. Sorry if I wasnt clear. I have bad grammar D: