How to reproduce:

1) Add a file A to private files and save.
2) Make a folder F in a course, and edit files
3) Add a link A2 to the file A, in folder F
4) Add a file B from wikimedia to the folder F (it is copied)
5) Save the filearea F and reopen
6) The wikimedia file has been replaced by a second copy of A2 (except the name).