I completed the Dex while missing 3 Pokemon

I randomly decided to talk to Professor Sylvan and she told me that I completed the dex and gave me the shiny charm. I went to the mysterious spire and found the Pokemon inside. I'll attach proof that I do have the Pokemon and am indeed missing the 3 pokemon while having the final pokemon. I didn't hack or try any exploits, I didn't even change the date on my PC.