I don't know-maybe they have had an audit or discovered a general problem. I think it 's always a good idea to keep a check on our tax at the end of each tax year
It might be that you wife has not earned enough money (to get a tax rebate) through an increase in her tax code.
Normally any over/under payments are corrected through a change in your tax code – but if someone is not eligible to pay any tax, increasing their tax code has no effect. After a few years (and realising that the money is still owing), this will be addressed through direct payment.
gingejbee is spot on. For decades they have had separate computer systems that did not "talk" to each other. Now replaced by one that is capable of reconciling years back.