Photos for Mac won't remove or merge duplicate images

Give this a try: As a test launch Photos with the Option key held down and create a new, test library.  Import a couple of the same photos and test to see if the same problem persists. Does it? This tells us if the problem is limited to your current library or is more wide spread.

Then try your original library again.

Regardless of the results above boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

Hi Andrew Strugnell,

Thanks for coming to Apple Support Communities for help today.

It sounds like you are properly following the steps found here: Remove duplicate photos in Photos on Mac.

Have you checked the Recently Deleted folder to see if they are there and permanently delete them?

If that doesn't explain the issue, please contact Apple Support for a deeper dive.

Have a fantastic day!