ok so my AR allows me to enter into mthe game with a code length of 2 pokemon. So I had to do 2 pokemon at a time. This should help those with the same problem (remember if u generate with the 2 selected in pokegen. The spots in pokegen will be used for the pokemon... ex)
your team-
aa
bb
cc
dd
ee
ff
Pokegen pokemon-
a
b
c
d
e
f
If u select pokemon a and c. In your game, spots aa and cc will be replaced. If u choose e and ef, slots ee and ff ingame will be replaced