I think I know the glitch you're talking about, so I took a photo of it. Is this it?
If so, then I've actually ran into it tons of times. It happens whenever you keep tapping the speak/interact button while leaving an area. I'm not an expert or anything, but what I think happens is that the game tries to load the "Nothing unusual here" message into the current town/dungeon/overworld, but since you're leaving the area, the message somehow gets loaded into the area you enter next.
I don't think button mapping has anything to do with it since I've tested it on the iPhone version (which has virtual ABC buttons) as well as Sega Genesis Collection (with the controls set to ABC mode) and the glitch worked on both of them. I don't have the original cartridge so I can't try it on that.