Did you happen to refit it as a Flag ship or with a transport module ? If so, flag ship and transport ship have one citizen on them so it can't get out of the colony since there's only 1 citizen present on the colony.

I'm thinking you could refit it back to a non flag/transport ship ? Else you could try turning the world into a core world so it can have more then 1 citizen in orbit (if the world is core-able that is possible).

I wonder if you could send another transport ship there and see if you can move one citizen over. I'd think the easiest way though would be to refit it back to a normal ship.

Alternatively you could try to use a console command; not sure if it'll work though. Enable the console in the settings, then open it using ~ or which ever key you got set for it, then type hotkeys. Select the ship that stuck and press F1 while pointing the mouse on a nearby Hex. See if that moves it. Makes sure you save your game before trying this though !

Would you care sharing a save file with us so we can take a closer look ourselves ? Best place would be on the gc4 discord! Here's the link to the server: https://discord.gg/galciv 

@Draver

What I expect has happened is that because the survey module was added to an existing ship rather than fitted at a shipyard, there was no citizen on board. It worked perfectly well in deep space, but once it arrived at a planet, ANY planet, it tried to add the missing citizen. If this is the cause, then the ship would have been stuck, even at a core world, if there was not a spare citizen available to allocate to the ship.

I thought I had parked it at colonies previously (maybe not) without a problem. This may be because it was still an enforcer(?) when I did this, which is a special case, but after I refitted it, it became a standard ship and needed the citizen.

Wondering why a survey module requires a citizen?