Mandy Smithberger, director of the Straus Military Reform Project at the Project On Government Oversight, said some of the mistakes made by the Navy on big-ticket programs have been self-inflicted. The service's tendency to "develop really complex technology that's expensive to maintain and not reliable," has been a major drawback.

Added Smithberger, "It's not necessarily that it's new technology but it's immature so it has to be proven technology."

Some analysts said the new ideas for the next-generation ships originated in the 1990s, when there was a "go for broke" mindset by some decision makers.

In the case of the Ford-Class carrier, the Navy decided to make all of the key changes in new technology upfront on the first ship in the class, rather than wait for successive carriers. The Navy plans to spend around $43 billion on the first three Ford-Class aircraft carriers.

At the same time, the Navy and other services have faced fiscal challenges due to the ongoing effect of the budget caps signed into law six years ago.

"The Budget Control Act, as far as it pertains to defense, was wrong-minded and that should not have been systematically reducing defense spending," said Brian Slattery, a policy analyst for national security at Washington-based Heritage Foundation, a conservative think tank.

He also said the inability of Congress to pass regular budgets is "very disruptive" to Navy and other service programs.

For the Navy, though, the budget situation is particularly pressing because of Trump's stated goal for a larger Navy fleet.

As a GOP candidate last year, Trump pledged the Navy would build 350 surface ships and submarines. He has since accepted the Navy's new force structure goal of a fleet of 355 ships up from the battle force of 276 ships as of Friday.

However, reaching the Navy goal could cost approximately $400 billion more over 30 years than the service's previously stated force goal of 308 ships, according to the Congressional Budget Office.

Based on CBO's calculations, the Navy would need to buy around 329 new ships over 30 years to reach the 355-ship fleet. That compares with the 254 ships it estimates would be bought under the Navy's prior force goal.

"Cost is probably the biggest challenge reaching the larger fleet size," said Smithberger. "You'd have to increase Pentagon spending a lot to afford everything that they're trying to buy. It will require cutting other services or other Navy priorities, including airplanes."

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The Navy's put down a 'significant bet' on the $13 billion USS Gerald R Ford, which some say is a risky gamble - CNBC