Teams can only be unloaded at (your) colonies.  This isn't normally a problem with your ships, since the 'drop off team' order creates a colony if there isn't already one there.  Since you can't issue that order to a civilian, it can't drop off your team . . . automatically that is.

Easiest thing to do is exactly what you did, but after teh ship arrives instead of using SM to return the team to your homeworld, use it to move the team to the alien world.

So I noticed that any of my teams could transfer to a civilian ship in orbit, from the Teams/Academy tab.

"Brilliant!" I thought.  "I've got a meager trade route established with that empire next door, and this is a perfect way to slip an espionage team onto their planet without raising any suspicion. " And it seemed like a nice in-character way to do it, too.

Problem: Once the freighter arrived, I had no way to unload the team.  The team doesn't show in the Teams tab once it's aboard a ship, and I can't give the civvie orders to drop off a team.  >_<

I wound up using SM mode to reset my team members back to my capital, so they weren't stuck permanently plying the spacelanes, but is there something I'm missing? It seems odd to have the option to transfer a team to a civilian ship if there's no way to transfer them off again.