Inconsistencies in file sorting

[bowlerhatman]

I've been using phockup to try to sort out my mohoyo collection. On an early attempt, I noticed a weirdly low number of photos for one year in particular (2016). There were something to like 300-400 pictures in the output dir /2016. Looking into it, I could see that I had taken many more than that. Some had been downloaded from Google take out, and some taken from my phone SD card, so I had two folders for 2016, sorted fairly randomly.
I then put the whole /phone directory through phockup and separately put /google through.
I had 911 images in /google and about 80 in /phone.

I then sorted the two directories at the same time through phockup, and ended up with 901 images in /2016.

Clearly there was some duplication, but I'm struggling to understand how on my first try I had only 3-400 images. I'm also struggling to understand how on my latest test the final number of images could be lower than the larger of the two numbers? In other words, if I have 911 images in one folder, and I intersort them into another folder containing 80, skipping duplicates, how do I end up with <911 images? Finally, how could these two approaches be so different in result?