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I have a lot of Apple products that all sync together and I had this issue.
This is how I fixed it:
Took the device with the correct counts and put that aside. Went to all the other connected devices, Macs, iPads and iPhones and turned off iCloud photo library. Once it was off and not syncing I deleted ALL the pictures and videos on those devices. I removed the recently deleted as well so they really had NOTHING on them. Make sure iCloud Photos is OFF before you do the delete step. To play it safe reboot all the devices you turned it off on and wait a bit to clear it all up.
After you only have one device with photos and connected to iCloud Photo Library, start turning on one device at a time and wait until it completely syncs. Once it is in sync move on to the next device.
I did that with all of my devices and now everything is in sync. 2 rMBPs, 2 iPad Pros, 3 iPhones.
