When copying a file, and then undo-ing, it would warn that deleting the file would be permanent. However, it was said that it should only be trashed, especially since redo-ing would undo the delete, which the message said you couldn't do.
To fix this, I tried to hunt down where it was coming from. I realised that it was calling delete, instead of trash_or_delete. I read the functions, and delete only seems to be meant for permanently deleting the function, whilst trash_or_delete... trashed or deleted. To test my theory, I swapped it over, which seemed to work.