Apparently there's a difference between constructed roofs and ship roofs. You can't build ship roofs, but they get built automatically when a room is fully finished with hull panels. Even though it doesn't make much sense, try removing the roof in the room that says it's unroofed (Zones -> Remove Roof Area), then ignore the roof area (Zones -> Ignore Roof Area), then deconstruct all of the hull panels (the floor, not the ship hull walls), and lastly rebuild all the hull panels. The pawns should automatically rebuild all the ship roofing and seal the room up.

You can also move the ship or load the saved game again.

That unroofed tile happens when 1.3's stupid shuttles crash through the roof, and our system doesn't check roofs until a big event like a save is loaded or the ship moves.

I found a way to fix this same issue actually on accident.

whatever room is "unroofed", just use the remove floor command on all the hull plating tiles in that room. also, check your roofing zones and make sure you use the "ignore roof" zone everywhere in that room (entire ship actually should have Zero roofing zones.

do not use the "remove roof" zone in your ship at all, or you'll have to do this whole process again.