I've never heard of a glitch like this, but that doesn't mean it doesn't exist. Try a few things to make sure you're not mistaken, and that you actually do have Hippowdon registered in your Pokedex.
- Check that it was actually a Hippowdon you caught.
- Make sure you're looking in the right pages of your Pokedex. Hippowdon is #450 in that National Pokedex, so make sure you're actually checking around there.
- If possible, catch another Hippowdon and see if it was registered.
- If three wasn't possible, breed the first Hippowdon, and evolve the Hippopotas you get into a second Hippowdon. Check if it was registered.
If all these are unsuccessful, then I have no further possibilities as to what happened. Hope I helped!