I remember in the book "Skunk Works" by Ben Rich, he talked several times about how if they ran into issues or messed something up, the government made LM cover the costs. On the other hand, if LM came in under budget (which would probably never ever happen these days), they would reimburse the government the savings. What has changed?
I know he cited exponentially growing beuracracy as a huge problem. I don't remember the exact numbers, but he said something like only a couple hundred people were involved in developing the U-2, versus thousands of inspectors, etc, and millions of pages of mostly useless paperwork generated PER DAY on the F-22 program. I guess it all adds up to a huge amount of wasted money in the end! And that was in the 90's; it's probably only gotten worse since then.