UPDATE:
The Desktop Uploader app has now been replaced by Backup & Sync, but the new app is also plagued by a duplication issue (not sure if the root cause is also same).
Original story below:
Though Google Photos comes baked with identical duplicate detection feature which inhibits re-upload of same photos, the functionality doesn’t seem to working as expected for many.
The problem was first reported in March, 2016. Some users encountered doubling of all pictures, while for some it was two or three copies of few pictures when using desktop uploader. On November 9, 2016, an expert at Google Product forums stated:
“Nothing seems solved. A bug report has been filed but we never get feedback before a bug is fixed”.
On June 15, 2017 another expert further added:
“Google must know about this problem as several months ago I had a survey from them which asked many questions about whether I was experiencing duplicate photos”.
It seems that despite being aware of the bug, Google neither acknowledged nor bothered to fix it. A quick look into official Google Product forums and a thread on Android Central reveals that this issue still prevails.
Some of the users have figured out workarounds that fixed the issue for them. However, the suggestions appear device specific. One of them has suggested that moving pictures between device and SD card generated duplicates. Disabling Auto-backup and manually uploading the images (only after the pictures have been successfully moved to SD card) resolved the issue for her. Another user shared that disabling ‘Automatic creation of events’ in Samsung Galaxy S6’s gallery application barred duplication in his case. And finally, one of the users mentioned that disabling ‘Motion photos’ in their Samsung Galaxy S7 Edge fixed the issue for them.
We are unable to confirm any of these workarounds at this moment. But you can surely give them a try.