I guess the question is do these bugs happen in ZSNES with the original game? If so then I wouldn't worry about it.
Yes. With the savestates I have, I can use them with the original game and the same things will occur. When using SRAMs the same thing also occurs in both versions. BUT.. in either version, if you reset the game or load the ROM fresh, then load your save game, the problem will go away. That's why I can't just transfer the SRAM to another emulator to try it or debug it. Loading your save game without resetting will not fix the issue.
So, it's difficult to say. It's probably going to be next to impossible to fix and damn hard to figure out if this is emulator related or not, other than the fact nobody has ever had these issues on the real hardware or BSNES so far. The game itself might also simply be buggy.
I guess I'll keep waiting and see what other info might turn up.