In Super Robot Wars A Portable, there is a scenario boss that can join you later and when you manage to Ace him(get 50 kills and you get a unique ability for him) he gets ridiculously bulky the less health he has. That sounds helpful but that ability carries over back into his NPC Boss form in NG+ and I’ve heard it soft-locks the game.
Only way to avoid it is to know that information and don’t give him kills.
Some of the most iconic pokemon red/blue glitches were due to oversights, the iconic missingno glitch is based around the fact that the tiles you encounter it on just… don’t have encounter data programmed in.
A lot of the issues with those games are due to the gameboy hardware being ancient and the carts being too small for any kind of memory protection, but there’s also some just outright oversights.