I remember Richard Bowker saying that no one person knew the reasons why WCRM (unfinished and reduced scope) cost in excess of £8 billion instead of the £2 billion estimate.
Being a veteran of that campaign too I can offer a few guesses! Originally promised to Mr. Branson as a 140mph upgrade (PUG2) it got repeatedly de-scoped as the various subprojects discovered some really
really good reasons why 140 (and then 125, PUG1) wasn't achievable (without lots of money and a hybrid bill, anyway).
During this recidivism no-one kept track of what the result was going to be, so at the 11th hour scope had to be put back in, in compressed design timescales and poor possession access / late notice blockades, which drove the costs up.
On top of this the American programme management consultant was driving (think whips) everything and everybody so they would get their completion bonus (which they did), riding roughshod over things like working hours, common sense and actually delivering a proper result. In terms of "PUG" I think we ended up with PUG0.7-ish. There are still things not done ...
In summary, the initial scoping and costing was skimped (if it was done at all) which meant that when it came time to spend there was always going to be a gulf; same with the electrification projects. The best time to spend money is right at the beginning, as an extra £500 spent thinking about things back in the "hey kids, lets electrify the railway" stages of development can save up to £8m later - and that's a real example.