EDIT: Here's a 1992 GAO acquisition study[1] on the AN/BSY-1 combat system whose development started in 1980 and was an absolute clusterfuck for the Navy in the decade that followed, as history would have it. I originally learned of this disaster from a former sailor (and now good friend) who participated in sea trials for one of the submarines that this system was installed in. By his account, the submarine had had its hull recut just to get the system installed and routed properly, and it never really worked as intended. The study vaguely alludes to this:
> As a result, the shipbuilder was eventually faced with rip-outs, recutting of hulls, and rerouting of cables.
Electric Boat was the prime and responsible for system integration. They've had their fair share of glorious fuckups to the tune of $82.4MM in late 80s dollars, so it's funny to read the hero part on how they've "helped other countries with their submarine programs".
In the right professional circles, stories like these quite literally abound. Now what's the probability of learning about them without the internet?
Cliff Stoll's rememberance is interesting, though doesn't discuss errors:
http://gen.lib.rus.ec/scimag/?q=stoll+When+Slide+Rules+Ruled