Funny that these things are mostly referred to as 'emulator bugs'. It would be more accurate to call them bugs in the game.

It's a bit like the situation with C, where some code depends on a specific outcome of undefined behavior.

With this, I don't mean that the programmer of the game is to blame. If you are developing for a single system, it is reasonable to use some of the properties of this system. In this specific situation, it might even be of interest for Nintendo, since it makes it harder to pirate games.

If one would like to avoid a situation like this, it seems best to develop for an emulator with unreliable properties (the principle of fail-fast: crash and let the developer know that he makes an assumption that is not guaranteed to hold), but which implements the ISA faithfully.