Re: The boss owned up? Apologised, even?
I actually had this happen when I was in the military.
I was on a submarine for about 4 years. At the time, I was one of the most senior people on board. The boat was a fairly new class of submarine, and had a different kind of propulsion plant than most of the rest of the fleet. Our engineer had moved on (with a promotion) and so we had a new engineering officer who was pretty 'green' with respect to our power plant. Some of his decisions reflected that, telling us NOT to do things we've always done before etc..
Well we were running engineering drills for the upcoming annual examination, and because of a stuck valve, I was told (by the engineer) to do something that violated a procedure. It posed no actual danger, but it violated the procedure. So I told him that (but I couldn't remember where in the procedure it said NOT to do this, I just remembered it). He said to do it anyway. I offered alternatives that were allowed by procedure. He said "I'm not going to XXX because of YYY". I asked for a watch relief. He got angrier, said we weren't going to do that in the middle of yotta yotta yotta. So I logged that the engineer ordered me to do that thing, and I made DAMNED sure it didn't pose a danger to human lives or equipment (it was only for about 10 minutes anyway).
Then later, it really bugged him that one of his senior people would be so insistent (even though nobody else was) so he went looking for where it said NOT to do that, and discovered that we were supposed to shut down the reactor under the condition he told me to operate it under [remember there was no actual danger, I made sure of it]. Well, somewhat embarrassed by this, he did the right thing: he called me in personally, apologized, and then held 'all hands' training on it. No doubt an 'incident report' was also filed. [again there was no real danger, it was just a violation of the procedure, which was intended to protect against a different possible condition that wasn't present, and would NOT be with my hand on the controls]. And of course, we didn't get the engineering 'E' award that year, either [but didn't fail our annual exam].
Unfortunately, the engineer wasn't any easier to work with after that. He was actually a bit [more] overcautious. He should have trusted his people more. But I was the _ONLY_ person in the engine room that understood that what he wanted us to do was against the procedure. Had I said nothing, we would have FAILED the annual examination, which is a _LOT_ _WORSE_ than what happened.
And it wasn't THAT bad of a situation, because if it WERE, the engineer would've been 'fired'. He wasn't. He actually got promoted on schedule, from what I understand. So yeah no danger, just an "I *blanked* up" on his part.