Are you talking about placeholder pokemon like Missingno? They only exist because of the way data is stored. Correct me if I'm using these terms wrong, but 8-bit meant 255 bytes or pokedex entries could be stored, and 16-bit, the next step up from 8-bit, could store 65535. In the gameboy generation one and two games, there were a few empty slots that had very glitched entries that did exist but were not technically 'valid,' I guess. Invalid entries still exist in oras and I'm assuming Sun and Moon although I haven't checked it yet.
?????????? was just another placeholder would be my guess for an 'invalid' pokedex number.