Actually, it's not a glitch. The Pokemon you've seen with the highest dex no., e.g Shaymin, which is #492, will be at the bottom of the dex list. If you've seen arceus after you've seen Shaymin, then a new entry will be filled in, here's an example with the sinnoh starters:
Since you haven't seen any other Pokemon, then it won't be filled in completely. Hopefully this answers your question. Hope I helped(ish)!!