I have also had hundreds of duplicates created by the sync process - so many that I have started keeping a spreadsheet where I capture the counts before I sync on the FTM tree and my Ancestry tree, then very carefully check the Sync report before going forward.
In the sync before my last re-download, I noticed that it wanted to attach the same photo to many people that it didn't belong to, so I tried the option to use the backup copy of my FTM tree and relink to my Ancestry.com tree. In doing that, I lost the setting to link all of my preferred photos on everyone in my tree. That affected thousands of people - with no indication to warn me that might happen. I'm fixing them as I work on my online tree. I also lost a whole bunch of media that went with my FTM tree.
Still very cautious whenever I do a sync.