Bashaamo in RSE throws fire rays from between its legs. In DP, Beadull uses water gun from the back of its neck.
In HGSS, the Trainer sprite is for some reason placed behind the Pokemon, while the Trainer sprite and the Pokemon sprite switch, so the Pokemon always look smaller than he Trainer, even Pokemon such as Lugia.
And Pachirisu is very big in double battles.
In Colloseum, there is a glitch that make some bird Pokemon stand still in the air sometimes when they use the Fly attack.