The same story was presented today as:
Telegraph - "1.2 million owe tax after HMRC error"
Accountancy Age - "PAYE reconciliations show sharp improvement"
The latter is much the fairer headline. HMRC are supposed to check each year whether those on PAYE who don't have to submit a tax return have underpaid or overpaid tax. Over the last few years they've done a horrible job of this. For 2010/11 they seem to have done miles better.
The existence of a lot of people who didn't pay the right amount of tax via PAYE doesn't in itself constitute an error on the part of HMRC. Sometimes they just don't have sufficient information to sort someone's tax out until after the year's finished. That's completely normal.
So, on this occasion, HMRC are right and the Telegraph headline is wrong - though it should be noted that the content of the Telegraph story doesn't really match up to the headline, being more even handed.