Yes, I've also found this to be 'standard behaviour' when using TreeShare to download the 'same' fact to a number of individuals, e.g. Census data. Also reported it a number of times during the Testing Phase, but never saw any acknowledgement or improvement. I was preparing to report this on the Forum together with a few other quirks (see below) but you beat me to it.
At present, the only option (other than allowing the continuous proliferation of duplicate media) seems to be to keep a regular keep watch on the media folder, delete the duplicates, and then manually 'correct' media tags/links.
The occurrence of duplicate media can be reduced, but again only (at present) through manual intervention, e.g. when you know that a fact/source media downloaded affects a number of individuals e.g. a Census Record, add the entry to the other individuals and use Memorise and Paste to add the Source(s). However, I've found that some of these additions also require some editing of Source Detail, e.g. for Ancestry Source records that do not identify a Family Relationship (Census Records/Passenger Lists etc,) the "Source Details" often include a different line number for each individual on the image page which makes every citation for that image different. There is a similar issue where multiple families of interest appear on the same Census Page.
Must admit that I experienced the same issue from time to time with the 'OId' Ancestry Sync procedure, so was aware of the potential for this problem. Not sure if FTM 2017 suffers in the same way as I haven't tested. I suppose the main issue is to understand whether this is a current limitation of the API, or if there is any way for RM to check and warn users of 'apparent' duplicate media. - It would, presumably, be considered poor practice to simply overwrite existing media with the same file name, as they may not be identical images, hence the image file names are altered whilst ensuring that the image files remain in a logical sequence, thus highlighting the problem.
Additional Duplication/Other Issues:
- Duplicate Ancestry Sources appearing in the Master Source List - These cannot always be cleared with 'Automerge' so often have to be merged manually.
- Place List needs constant attention/management/pruning because of the multiple ways Places are recorded in Ancestry's data sources.
- Data drawn into RootsMagic from the Ancestry Fact Description Field may be visually useful, but make little sense in RootsMagic reports when left 'as is'.