In the white tree hollow some of the Pokemon I battle don't register as iv seen them in my pokedex while it seems some do. I can note specifically togekiss. Is this normal?
Yeah. Totally normal. Pokemon you see on things like the White Treehollow, Battle Subway and Wi-Fi Battles don't register in your Pokedex.
Pokemon that you seen in White Tree Hollow / Black Tower are not registered on the Pokedex.