Post a track file if you're able to duplicate it. I suspect your internal wings are full when you are trying to refuel, and despite the remaining fuselage fuel being low, there is no place for the fuel to go as the refuel floats are up, and shutting off the refuel system.
I tried to see if that was the case in the video, but the person flipped the FUEL QTY switch too fast through the INT Wing position.
If the externals have fuel, and feeding it is very likely the INT wing is full. In this scenario it isn't a bug, and you have created a scenario where trapped fuel will soon occur.