The MTA claims that New York City's transit system doesn't have enough funding to keep up with requirements. Critics of the MTA claim that the transit system has more funding than ever, and just isn't keeping up because of some vague inefficiencies or incompetencies.
This is the exact same argument that we have when it comes to education, health care, defense, and so forth. Some argue that it's because government spending is inherently inefficient, and while that may be true, that doesn't explain how governments outside of the United States still seem to be a lot more efficient than governments inside the United States, nor does it explain similar phenomena in things like housing.
This seems like a very broad problem that is currently beneath the public consciousness. SSC's "Considerations on Cost Disease" (http://slatestarcodex.com/2017/02/09/considerations-on-cost-...) is the first general discussion I've found of this, though Scott Alexander cites a paywalled Tyler Cowen piece in Bloomberg.
(Fair warning: while SSC doesn't mention defense spending as an example of this, the US has a ridiculously high defense budget without actually having the quantity or quality of troops and ships and aircraft that such a budget would imply. If China's defense budget were the same as ours, they would whip our ass in a conventional war.)
Whatever the shared root cause or causes are, they need to be addressed. Just giving MTA, Medicare, the Pentagon, universities, etc. more and more money isn't going to be sustainable. And, despite the ramblings of certain conspiratorially-minded folk, I also don't really think this is inflation in disguise, because then you'd also have to explain why there hasn't been a corresponding increase in the costs of e.g. basic groceries.
I don't have any answers here; I just don't think we're asking the right questions if we just restrict the discussion to the specific areas where we see this happen.