Not really a bug, more an artifact of how national limits work. It does mean that if you recapture the city you can have 3 contracts, but that's also true if you captured an enemy city that had a landing stage.
I guess we could have made it such that landing stages and contracts were destroyed on city capture, but that could have messed up other things.
Anyway, glad you're playing the mod, I hope you're enjoying it. I hope you like that the game can be tough enough that you lose cities!