In my experience these underpayments and collections are entered manually by a Revenue agent and they can sometimes get them wrong. I have used the My Enquiries to get them corrected. Do a manual recalc of what you should have paid and compare to what you did and you should see it. My issues arose when I changed jobs and tax credits weren't reassigned correctly, not sure if that is the case for you or if it was an underpayment by your employer which needs to be settled by you.