It wasn't noise-cancelling not being perfect (it worked just fine), but noise cancelling going bonkers when the earmuffs come into contact with another solid object (in my case, neck cushion on seat). I think it broke the around-ear seal a teeny bit and that threw the noise cancellation off.

Right. I'm saying even when used correctly, it wasn't protecting your hearing from the noise of the flight. Notches of noise were poking through the filters despite the impression of quietness, and causing fatigue damage to the cells tuned to those frequencies.