Niantic has updated an official known issues support page for Pokémon GO. Read on below to learn more:
Pokédex “Seen” count inaccurate for some Pokémon
Last Updated: 2h
Issue Description: After encountering Groudon or Kyogre after defeating Primal Groudon or Primal Kyogre in Primal Raids, the “Seen” count for these Pokémon in the Pokédex doesn’t increase.
Issue Status: Working on a fix
Source: Official Pokémon GO support page