Times in games when passing skill checks doesn't have the best results?

Generally in video games, if there's a skill check that you can pass, that's the correct answer. Sometimes that's not the case, and I find that way more interesting.

An example would be Dean Domino, the ghoul from New Vegas' Dead Money DLC. You meet him when he puts a bomb under your chair, and he threatens to blow you up.

If you have high skills, you can point out how much of an awful idea that is. However, Dean Domino is an asshole, and wants to feel superior. Doing that makes him hate you, and locks you into having to kill him later in the DLC. If you want him to live, you have to play along and just agree to his demands.

Now, whether or not you consider him living to be the "good ending," that's another question entirely.