I have just got off the phone with tech support who said there is no fix for this problem so I thought I would warn others...
I recently experienced a sync problem which required me to load a backup tree and upload to Ancestry to resync the FTM and ATM trees. At the time sync was okay but shortly I began to notice sync failures and I would get a "retry" button if I clicked the failure notice. I looked in FTM Media and discovered several media place holders (no files) with the same file name. Then I discovered that recently downloaded media had created a second source group with the same name (duplicated group). Worse, the duplicate source group had been uploaded to ATM so when I look at the ATM source list I now see duplicate sources which I suspect are now contaminated.
And it gets worse: The FTM Media place-holders with the same name (file number) should have different media images. I had six 1860 census media place-holders all ending in the number -396 but each should have been a different 1860 census image. All were located in the duplicate source group and none had downloaded image files, just the place holders. Inspection of the primary source group disclosed the last image was -395. Attempts to download the missing images in the duplicate source failed.
I can't be positive but I think this problem was caused when I edited the source group by adding text to the "Comment" field. This probably caused FTM or ATM to think the original source group no longer matched so a new (duplicate) group was created.
I have a couple hundred media/source citations to clean up so I hope this helps someone.