Yeah, this is already heavy bugged. You have two options, the easy one is to choose Edit, and Clear all overworld sprites. Then save and hope it is fixed. If not, you need to debug this using the hex editor. Go to the overworld sprite hex code and empty it manually.
Also, if you are unable to debug using the hex editor, you might want to wait untill Math On Napkins finishes his Black Magic Alttp editor, or make more constant backups, to be able to return to a previous version (which didn't have this bug). You might also want to test this in-game, since it doesn't seem, that this version is playable.