There are many issues here:
1. Generally to win a contract you have to be the cheapest, so they are often pitched at an unrealistic price to win, knowing that pay more or we don't complete half way through puts the contractor in the driving seat. If you don't choose the cheapest you have to put forward a good case why, which may well be overruled, by somebody higher up the chain.
2. What is proposed for the price won't do the job, but the Government does not have people with the knowledge or skills to do an objective appraisal of what is being offered. This is especially true with IT contracts and is a reflection of the cheapest price wins.
3. Feature creep and changing specifications by the Government. The aircraft carrier procurement has been hit with this much more than other projects, and there has also much party and constituency politics, this becomes more onerous the larger the project.
4. One or small number are required, so there is always an R&D risk with known unknowns and unknown unknowns. This particularly applies to the specification of military equipment where you are striving to have the best and most advanced you can afford.
5. Government and civil servant incompetence, why should they care it is not their money, easy come, easy go. We see this where the technology and risks are not ground breaking with HS2, NHS patient database being good examples, but there are many, many, more.
6. Contractor incompetence, this can occur at any level from the top to the bottom of the organisation.
7. Gold plated specifications and whole of life support.
8. Government contractor regulations, HR and H&S requirements are normally quite onerous, which pushes up costs.
Unfortunately, where we see this happening time and time again, it is obvious the system needs reforming, but politicians don't seem to have the knowledge or will to do this.