From the start there was the idea of one aircraft for three services with a STOVL requirement and stealth was a huge gamble. Then, inexplicably the DoD decided that instead of providing detailed requirements for the platform like they usually did, they would let the contractor write many of the requirements since 'they have the expertise in building warplanes'.
Then, on top of that they decided to implement concurrent development, where they'd be doing testing and verification of the aircraft in parallel with production. In theory this would save time but in practice the reason you do testing and verification before production is to avoid expensive retrofits when problems are identified. Of course, many expensive retrofits have resulted.
On numerous occasions performance requirements have been lowered, deadlines blown, and the cost is tracking to be so expensive that it's making the F-22 look like a bargain.
Then there's the fact that production of parts of this program are spread out over 47 states, meaning every Congressman has incentive not to stop this runaway freight train of waste and negligence.