I'm using 3.0 stable, today I tried exporting and I got that error. Since that never occurred to me, I searched for clues here, but, as mentioned in a couple of questions, re-generating the keystore didn't work.
After a bit of struggling I found out the error was due to the fact that I had previously renamed some assets inside the editor, but I did not notice that Godot made a copy of the file with the new name, keeping another copy with the old name.
Basically I fixed the error by deleting the old copies: somehow having the same textures with different names breaks the exportation process. Is this normal or a bug? Should I raise an issue on GitHub?