Pikmin

Some enemies relinquish pellets after they are defeated. Do they swallow pellets whole and do they remain undigested in their bodies? Actually, this one can be answered. Shigefumi Hino, Planner for EAD and Pikmin Director, said this in an interview with Nintendo Power: "The creatures ate them. (Laughs.) The reason a pellet comes out is that the things the creatures eat turn into lumps of nutrients and they stay in their stomach."
If you leave flower pikmin in the ground too long, why do they sink into the ground, disappear, and then remerge as leaf pikmin?
In order to find certain ship parts, you must defeat certain enemies. How did they get inside those creatures? I mean, there are some parts that are as large if not larger than the enemy it was inside.

The front of Captain Olimar's ship looks like a pokeball. Another shameless plug by Nintendo? Or is it a coincidence?