As far as I remember they give you the "don't have landing gear" error if you try dock them from their cockpit, like some other things, so gotta tractor them. They might have fixed it though, been a while.
Moons can't fly.
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You need a tractor beam to dock containers. I moved some recently and only could use a tractor beam. Epods can lightravel, thats why you can dock them, but containers can't travel, and thus not dock themselfs.