This happens in online multiplayer.
As you can see, I have a giant standing on a port without becoming a boat. It remained this way after ending my turn & reopening the game.
Some relevant history of this turn:
- I have converted the other giant on this turn from gray to my team.
- I captured this city this turn from gray with the water walking giant.
- I leveled it up to create a super unit
- The giant got pushed there by a crab spawn.