Besides that, the cost of the program is way over budget, the resulting aircraft is less capable than what Lockheed-Martin advertised and promised the DoD to win the contract and is years late in actual production and deployment.
The F-35 program is symptomatic of larger DoD acquisition problems, an aircraft carrier that was to cost $8-9 Billion is now going to cost ~$16 Billion and is running 4 years late
Seems to be no different to the civilian counter parts projects. There has been a few studies revolve around how large projects are seemingly always way over budget and time in the western world.
I'm gathering its starting to be standard practice and the multinationals figure it in their project costs.