I've noticed a few pokedex sprites missing and even one pokemon that's in the game that isn't even listed.

Fenniken is not listed in the pokedex.
Girafarig has no normal, shiny or ancient sprite.
Magmortar and Electivire have no ancient sprites but are obtainable via evolution.

1) I think Da Man is just waiting for other pogeys to be added, but, I agree, it should be there.

2) No comment

3) Magmortar and Electivire are 4th gen pokemon, so they have no ancient sprite. Unless he uses a sprite that someone else made and such, it can't be implemented.