- The USS SEAWOLF -- SSN 575, not the badass SSN-21 -- used a liquid sodium reactor that was plagued by reliability problems. After its first deployment, the reactor was replaced with a traditional PWR.
- The USS JACK -- SSN 605 -- was unique in that she had contra-rotating propellers. These were generally unreliable, although the linked wikipedia reference doesn't say much about them.
- The USS TULLIBEE -- SSN 597 -- had electric drive.
- The USS GLENARD P. LIPSCOMB -- SSN 685 -- was the second attempt at electric drive. But both of these boats ended up being heavier, slower, larger, and more expensive than their counterparts.
- There's another submarine, I can't remember which one, had some unique aspect of its turbines, which was not effective. It was SSN-6XX, but its nickname was building 6XX because it was in the repair yard so frequently.
In the grand scheme of things, the above hiccups are a miniscule portion of the overall fleet. The Zumwalt ship is one of three in the entire $22B class. So, I think the naval nuclear propulsion program has been blessed in that it has been able to experiment and occasionally "miss" with some new technologies without threatening the entire endeavor.