They were on that 5x10 sheet shown during the Heisei era special.
Granted Lapras was on it twice and Charizard, Noctowl, and I think Poipole (it could have been made before Poipole was caught) were absent.
They could have just been being thorough by including the rat, the bee, and the fish, but leaving out Charizard and Noctowl and adding Lapras twice? That's really odd. Someone did not double check their work.
Actually counting those three with everyone including Nebby and Larvitar would make it a solid 60.
Difference is he never actually caught Nebby and Larvitar in a ball and as such were never his to begin with.