The first candidate I'd propose for the top slot is diffusion of responsibility stemming from a US obsession with localism. An MTA project might well be paid for by: the federal government, NY state, NYC, and bonds to be paid back by a dedicated tax in 10 downstate counties. There are contracting rules imposed by each of those sources. And it is administered by the MTA board, a monstrosity with appointments from eight different sources. The buck stops nowhere.
The second candidate is, paradoxically, the progressive era procurement rules designed to rein in corruption. They leave too little discretion. In a two sided competitive game, if one side is hampered in by slow changing inflexible rules the other side is going to dominate. That's exactly what happens. Government contractors play the system like a fiddle and there's little the government negotiators even when they are supremely competent and diligent can do about it.