I have a broken save file. I went into Shrine 5, but ran out of rupees so had to leave. I save and quit back to game start, did the sidequest to get the coal to get 999 rupees, and now when I went to open my menu to give the NPC the vial of wind once more, I found out I cannot close either the menu or the map screen without getting a Kernel error and cannot proceed further.
I have the same problem, except when it doesn't crash, it warps me to the upper-left corner of the screen. Which has me permanently stuck in the final boss rush, since I can't damage the witch.
And sometimes, I do get a Kernel error. Other times, I get colorful garbage and the music keeps going. Most of the time, it's a white screen with frozen music.
I forego & skip the sidequest to get both the coal and diamond AND since I'm playing the game in the BGB emulator on my PC, I save & reload the game using only "save states" until I reach and beat Ganon; that is when I start to use the Save and Quit option. Only when I beat the game then I begin to get the coal and diamond items.
Do NOT use the "Save and Quit" option too much AND do NOT try to fill up the inventory with too many items (I mean do NOT buy the candle after beating the first two shrines as the candle item becomes useless after the 2nd shrine). that's when things go haywire.