The .gam.mast file tracks what girl files have been loaded in a savegame (you can open it in Notepad to see); so, for example, if your savegame was Brothel.gam, there would be a Brothel.gam.mast file as well. If that file gets deleted, it will be recreated when you load the save and all .girlsx files will be loaded into your game, creating duplicates.
The autosave doesn't create that file (I guess it probably should, though), so that's why it happens when loading the autosave. The safer way to load the autosave at the moment would be to delete your bad save file and rename autosave.gam to match the name, so it will use the existing .gam.mast file.