I had a similar nasty shock last year which I knew couldn't be right. Quick telephone call and it turned out I had made a major mathematical error in my calculations. 2 weeks later I had a recalculated coding notice, followed by a £ three figure refund.
PM me if you want the telephone number of a helpful HMRC Office in Leeds - the one I use, as a civilian as it is nearest to home. I always found PD4 helpful when I was serving.