Hello Eldrinn, sorry for the nickname typo, I know what it's like, trust me :)
Ok, I managed to reproduce issue even with vanilla game, and got a fix for it. There is a couple of items I still want to attend to before making a new release. One big warning - do not hit the undo once you deconstruct tiles like this at the moment - it will actually hard-crash the game (not sure if I should feel proud about this or ashamed) - at least it crashed Factorio version 1.1.61 for me.
In the meantime, you should be able to clean-up eventual mess created by this by using the /cp_cleanup
command - just make sure to backup the savegame before doing so just in case. The cleanup command should try to drop bogus deconstruction orders, as well as try to remove some inconsistencies around unapproved ghost handling.
Just a small side-note - specifying actual version numbers is more useful - latest can vary based on when someone reads the report :) But... Once again, thanks for reporting the bug, and I hope you enjoy the mod - as wonky as it can get :)