Hi, sorry, I’ll try to fix it.
Do you have the badge of having all mons?
Have you never seen those Pokémon before? Like, you didn’t obtain them and they later disappeared?
It seems like a weird bug, no one has reported anything like this. Until I know how it happens, I can’t fix it, but if you download your save .txt and send it to me via Twitter or Discord, I can manually add the Pokémon you’re missing.
19 days ago(+1)
I don't think I ever saw them, but I'm not 100% sure. I bought a whole bunch of eggs together at one point and didn't use most of them until much later. I'll see if I can send you that .txt, though.