Let me guess... you mostly work from the ancestry side? When saving records from the ancestry side, using the new merge tool for attaching records, new source groups were being added in FTM when syncing even though the source already existed (using the old tool, this did not happen). I had more than 40 SSDI groups (and that was after combining many of them manually. I complained about this over and over again, but no one seemed to get it. Sometime during the beta, I noticed that the issue had been resolved in 2012 and 2014. I had just collected screen shots and was looking to add a few ore before I reported it to the beta board... when it stopped occurring.
When I got the odd sync report, I was a bit concerned but I hoped it was a fix to duplicate sources. I emailed the dev team, got a reply from Duff, who was checking with the engineers. Before I heard back from him, I decided to back up and let it sync - then heard back from him saying they had implemented some fixes that was the cause of what I was seeing and it was safe to sync. Carefully comparison to the pre and post sync FTM files showed no loss of data.