The impression I've got is that the problems with the project come down to a combination of firstly, as @jgrahamc rightly points out, the fact the project has been unleashed all at once across the country rather than one surgery at a time as would be sensible, and secondly (ok, I am risking downvotes here bigtime), I think, poor programmer and management quality - I'm sure there are good programmers on the project, but overall it seems to me the quality must be pretty low. The damage one bad apple can do in software is immense and entirely out of proportion to their position, magnified if that person is higher up in the hierarchy. Additionally it seems obvious that the project has been somewhat mismanaged.

I do understand the project is huge and really very complicated, and naturally a difficult problem probably more so than is immediately obvious, but it is that very fact that makes it easy for poor engineering decisions to have a big impact.