You have to pay the bill in full now, state it is disputed in a letter and that you wish to take the matter to the General Commissioners of Income Tax where you can represent yourself.
Alternatively, you could take it through the HMRC complaints procedure. Eventually you will get to the Adjudicator and eventually the Parliamentary Ombusman. We did this but it took 2 years and eventually got the money as an ex gratia settlement but without interest.
Do not watever you do refuse to pay. You will have debt collectors on your dororstep and huge costs.
I've just had to sort something like this out. Made me want to scream.
I would keep calling back. Sadly, you will find, some people you speak to are enormously helpful and some people aren't. I would call until you get someone who can explain exactly why they believe you owe the amount you say you do.
If your dh is not financially minded, or an accountant, and he can't see why they are saying that, then I would suggest you do need some help I'm afraid.
btw, the student loan thing is appalling - I just managed to sort an overpayment of a student loan from one of our employees but my goodness, it was a challenge.
just watch the penalties and interest too - that could be adding a huge amount onto what you think the bill might be.
so is it his payment on account which is upping the bill? If it is, and if he won't be earning the same amount in 10/11 then he can reduce his payments on account - if it turns out when the 10/11 tax return is done that he should have paid the higher amounts, then he has to pay interest.