Not sure when it started to occur with the latest PKHeX, but I noticed that some Pokemon in Gen I JP games started appearing as Invalid due to the catch rate. These Pokemon have never been transferred or used in Gen II or Pokemon Stadium 2. The image I uploaded shows how it looks on the latest version of PKHeX (left) compared to an older version (20190919, right).
Guess it's due to PKHeX seeing the catch rate for these Pokemon as 255, which might not be normal? When I load a US Gen I save, the catch rate for these Pokemon appear normal (which is 173, which are Berries in Gen II) with no legality issues.