Manning problems have existed for a decade, if not more. The Navy holds the sad record of being the worst managed branch of service. Steep budget cuts in the 1990s and again during sequestration have had severe effects that the Navy hasn't yet recovered from. But I don't know whether that's the cause of the problem. The Navy is an especially unique branch given that it's the only service that revolves around a relatively small number of very large, very expensive assets. The Army doesn't revolve around its tanks, and the Air Force, while it revolves around planes, there are a lot more planes in the Air Force than ships in the Navy. Congress is not without blame for the Navy's problems either, apart from the budget cuts. Congress has the last word on all programs and procurement. The Littoral Combat Ships should never have seen the light of day for instance, but Congress pushed the program through, and now the ships are useless (and still being built!)
But there is hope on the horizon. The submarine construction programs (Virginia SSNs and Columbia SSBNs) are proceeding smoothly, as are the Flight III destroyers. DDG(X), the future replacement of the Arleigh-Burke class destroyers and Ticonderoga-class cruisers, is in development, and the first Constellation-class frigates will soon be laid down.