Trash is not compatible with manually sort folders options (in admin)

– There is an error when you try to empty/delete the folders in the Trash.

You cannot delete a parent folder

This is because the plugin only deletes the main folder post and not the descendant posts.

This is not an error, this is a message that you are trying to delete a folder which still has child folders.

Using plugin v.0.1.2 this is an issue when you have manual folder ordering option.

Looks like only main folders are trashed. Child folders are not trashed. This will give you the message when you try to empty the trash.
Unless changing the ordering option something else than manual.
… but child folders are not visible anywhere, because the parent folder already trashed.