With me no matter where I send my shuttles, they always circle. If you wait about an hour, they slowly spiral twards their target. I found, at least on land when picking up a mining drone, that moving the waypoint when the ship is over it causes the ship to fly down twards the new location. It usualy lands about halfway there, collects the drone, and lifts off again. With cargo pods, I just fly the ship myself to go get them.