The Pluto carries repair materials and ammo, while the Pterano carries fuel. However, I don't see why, because I cannot make the using it. Am I missing something?

You probably are. The Pterano may not move before refueling an Unit, and can only refuel Aircraft.

The Pluto can repair and supply Ships, but only if not submerged and not moved

Great answer, thank you. It´s a weird design decision and not "in line" with the rest of the refueling units, so I thought they were bugged and useless in that aspect for a LONG time.