I'd argue that the LCS cost overruns were caused by political interference: that 40+knot high speed requirement that never had a reasoning attached to it. It was just a "wouldn't it be cool if we had a 400ft ship that did 40something knots?!? We could zoom in and out of the littorals like a ski boat!" The LCS are faster than a carrier in a sprint! Anything over a couple day's travel and the carrier wins, since the LCS would have to slow down to refuel.
And so the boats are massively over-engined, and the Freedom-class gearbox just could not handle the power and broke all the time. Indys went with hydrodynamic trickery of the trimaran hull to go fast on less horsepower so they're mechanically reliable, but the aluminum hull tends to crack where the trimaran pontoons join the main hull due to wave pounding and flexing. And that's a pain in the ass to fix. Stop drill the cracks, then figure out how to (or even whether to) reinforce the sections to make them more resistant to flexing or make those locations out of more flexible materials that won't crack.
Ford is first in class, those always cost more than you expect.
What's the reason for the cost increases for the LSMs? Significantly increased weapons and equipment needed to survive in the Pacific? Like SPY6, Aegis, and a 16- or 32-cell VLS? That's called, "yeah, we really goofed on the defensive requirements in the initial concept. We thought these could be escorted by DDGs, but the threat has gotten significantly greater than we originally thought and the ships need FFG protection levels all by themselves."