Once you type the full name of a Pokémon into PC, it will show you as having x2 as many Pokémon of that species as you actually have.
For example, if I had 2 Snoms in my PC, and I used the search feature, I could type " Sno " and it would show I have 2 (the correct amount), but if i typed " Snom ", it would appear as if I had 4 Snoms in my pc.
Moving all of these 4 Snoms into an empty party, and you would see only 2 Snoms, and you might notice the other 2 Snoms disappear. I have also found this same issue with Charmander, but I have not tested beyond those two species.
I will attach two images that hopefully shows the issue better than I have described it. Because of the website I used the images will autodelete after 6 months.