In a PSA made by Benaclp, the lad revealed that there are some requirements that have to be met in order to complete the Kalos Pokedex. It is that all the pre-gen Pokemon must be born and raised in Kalos for it to be registered. Traded Pokemon won’t be counted.
The lad discovered this the hard way. Even after Benaclp received all the certificates and the Oval Charm, the Kalos Pokedex frustrates him as it does not show complete. After a thorough investigation, the player pointed out that his Buizel, which came from older generation Pokemon games, was the source of the issue. As such, breeding or catching the same Pokemon independently will fix it.
The entire Pokemon community are intrigued by what Benaclp discovered. For those who have yet to complete their Kalos Pokedex in Pokemon X & Y, this is some useful info that they need to keep in their mind.