The BBC article is suggesting that the flaps did not retract in sync .. that "they are not moving together" ... although quite how they got to that conclusion from the CVR is not clear ...
As normal practice is to retract in stages, I would have thought the imbalance would have become obvious before it became fatal, by the time you have a bootfull of rudder and the stick hard over, you would not be calling for another stage of flap retraction, you'd be thinking "hmm, that does not seem to have gone well" ...