Launched a rocket full of water pumped in from my rocket port. Built a new rocket, added and removed lots of parts, both exterior and interior. Didn't touch the liquid rocket port. Pipes were taking damage from freezing, liquid rocket port was farthest away, having to go through both a gas rocket port and a solid rocket port. Solid rocket port was not connected to input or output.
Sat for 20-30 minutes trying to fix freezing pipes, destroy and rebuild liquid rocket port, remove and add liquid tanks. Nothing worked. Quit out and loaded save, water starts loading in.
Seems the rocket ports can get out of the sync with the landed rocket.
Make rocket, add remove parts internal and external, try to load into rocket port, fail.