This has happened to me twice, so it's probably a bug.
I often move cargo around in order to make space in one ship (for example, to deliver a module which will be upgraded, thus freeing space again, or move a module which will be installed straightaway). When I do this, I usually just click on the items to be moved, including passengers and fuel, and type "9999" at the bottom box. 99% of the time it works fine.
However, twice already, my fuel disappeared in the process. Once I was on my orbital station in GJ, but this time it happened in Sol. I moved 2 modules (mining machines) plus 333 of fuel from one ship to another. The miners arrived fine on the second ship, but the fuel did not. I double-checked and had 0 fuel on the first ship, but only 40 on the second (which is what it had from before). There was plenty of space on the second ship.
I think maybe the bug is caused when the resource moved exists also on the destination ship. But it only happens when you combine the transfer with other things, like modules. If I move fuel back and forth on its own there's no problem.