SWMBO is a chartered accountant and many of her clients have suddenly received these notices - in her case she knows they are all mistaken, so it would be worth going back to challenge them to explain it further. But if they stick to it you will probably need to employ an accountant to prove it, and that will cost you a few hundred squids which is not recoverable (even if it was their mistake). But one fundamental thing - unless you are VERY sure of your ground it is better to pay it now, and then prove they need to pay it back - otherwise they will add interest and fines.
HMR&C is a low-pay organisation and few of their staff are actually qualified tax accountants - they make errors daily, and they don't care how much public money they dissipate in the consequences of those errors. Unfortunately there's nothing that can be done about that other than to spend your own money on a chartered accountant to act as your champion in the jousts...
PDR