You just have to ask the guy again - if you aren't able to get the certificates from the guy though, make sure that when you enter your Pokedex, there is a star next to Central Kalos Pokedex, Coastal Kalos Pokedex and Mountain Kalos Pokedex. If there isn't a star next to the first two then they simply aren't completed.
If they are and he still won't give you the certificates after talking to him multiple times, yeah, the game's glitched. However, the certificates are deemed worthless, and you'll only get an Oval Charm, which is not that helpful, really. Sorry.
Hope I helped. :)