That's no glitch. If you don't use a pokemon (or if it was nicknamed and never sent out normally, only dragged out with Roar/Whirlwind/DragonTail), it won't appear in the replay. You'd have to add it manually.
Holy crap this is awesome, i swear if you wrote a few analyses you would be a mod in like a second. But the thing that isn't working for me is that i get the same glitch as Tomohawk, I tried Google Chrome and Internet Explorer.