The start of the problem is listed in the second paragraph the Flight Global report:
For reasons that could not be determined, the aircraft's internal fuel-quantity indicator had registered the aircraft as a 777-200, which features a smaller centre fuel tank than the -200ER. This caused the aircraft's instruments to under-measure the amount of fuel on board.
So, it was wrong from the start and NO MATTER who did what it was always going to be wrong. No one would imagine that a/c 'thought' it was a different model to what it actually was!
Possibly time for some slack to be given.