The Garbage list is not only for bad movies, series or documentaries. It is also used for misspelled files names and so on... Put everything you don't want to have anymore in the Garbage list. If something is in the Garbage list MFM will not copy or move it anymore, so that there is no risk that you will get the same file again and again... If you have a copy of the garbage file somewhere else on your hard disk, it will pop up as garbage in MFM once you scan that folder.
Instead of deleting video files, move them to a "My Garbage" folder. Drop the My Garbage folder on the Garbage list, so that all names are remembered in MFM. After that you can delete the physical files.