It is unfortunately true in estimates by commercial companies for government contracts that estimates are usually low compared to the actual expected cost, usually I believe deliberately so as they think they can always increase it later and the government will pay. This is common in the defence industry. I was very pleasantly surprised to hear that the recent increase in the cost of new frigates is having to be born by the company . This contract was given long after the HS2 contract, but does at least indicate that there is some common sense being driven into the thick heads of government. That said, a considerable proportion of any increase must be inflation over the 3-decade length of incompetence. In addition land land was purchased for the Manchester link at probably inflated prices, much of which cannot be reclaimed as it is unlikely that it can be resold at anything like the purchase price, while "planners", who were presumably employed for that link, always seem to charge their customers many millions of pounds to carry out their work