Did your NJP come during the board process or was it sometime before you put in for STA?I did it, so.....I know at least one guy.
There's a big difference between:
-Sailor A who gets NJP early in his career, learns from it, and goes on to have a history of high performance past the NJP
-Sailor B who had good performance but then goes on to demonstrate poor performance that, per high level instruction, makes them ineligible.
Also, as others have mentioned, the board is VERY competitive. If there are 100 sailors up for 10 slots and 99 of the candidates have perfect records why would a CO send up a subpar candidate who won't get selected unless there's some sort of amazing success story in there such as NJP as an E-3 but has since made E-6 and become a cornerstone of the command (big jobs, collaterals, etc) that demonstrate the maturity desired for Officers. That's also not the case of a zero defect mentality, that's a CO being aware of the competitive nature of the board and what the board is looking for.
Also, I'm not sure zero defect is the same as toxic command climate.