Seems from the number of complaints relating to direct debits that VM made some changes to either systems or processes recently and for a small number of customers beggared up the payments resulting in either DD's not being called upon, or in this case being called upon but the systems believing they had not. Give it a month or so and check that this isn't showing as a late payment with the likes of Experian, because although the late payment has been credited back, it doesn't follow that the bad debt process hasn't already notified them of a late payment.
If a credit history check does show a late payment, then you should complain to the ICO about VM processing inaccurate data, and also complain to VM requiring them to correct the credit history.
