[CentOS] C7 Mate - files suddenly moved back onto desktop

My wife sometimes puts files on her desktop to work with them, then cut-and-pastes the file to put it into a folder when she's done.

This morning she has seven files on her desktop that she has worked on over the course of the past week. They have suddenly, overnight, moved out of the folders that she had put them into and moved onto her desktop! They are no longer in the folders that she put them into.

I told her to log out and log back in since I'm guessing that the Caja file manager may be somehow at fault.

Does anyone have any ideas about what else it could be? Some kind of cross-linking on her hard drive?