This happens to me on very clear occasions. I figured out at that time that, at least in my case, it wasn't a bug.
Planes are set to return once they reach a point of no return. If I move the ship and the planes, this "point of no return" changes every time.
So, when the planes get to that point and start to return... if I move them and suddenly the ship also closes in (closing the gap between fuel and distance to return), planes recover the chance of getting safely back to the ship... that makes the point of no return appear again and eventually, the planes will set the "no fuel going back" warning once again.
I know this is a very specific case and it might not be your case, but it happens.
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