I don't think YC itself was a bad choice for any of the startups I can think of; there were some cofounder disputes where one of the cofounders added negative value.
There were zombie companies, especially from after the START Fund was $150k (W11, S11, W12, S12) where teams which should have died stayed around due to YC; it might have been better in retrospect if they hadn't done YC and thus had the money to stay in hateful zombie mode.
I could potentially imagine a situation where a company would benefit from YC but would benefit more from it 6mo later, so e.g. doing YC W11 was a mistake and they should have done YC S11 instead; now I think some people are allowed to defer to the next demo day, which solves a lot of that.