An example that spring to mind is when a comment has missed the point of the context and so doesn't make sense but it is not important enough to embarrass the author by explaining or challenging.

I often do this myself (generally not respond to some comment to avoid embarrassing its author), but feel guilty and frustrated about it.

Frustrated: What if I'm wrong, either about my interpretation of the comment, or its merit (e.g., whether it really missed the point), or its importance? If I don't answer then I won't find out. (Of course a lot of the times I can use votes to help me decide, but sometimes not many people are watching the thread and all the comments in it are hovering around 0.)

Guilty: The other person may be wasting a lot of cognitive resources trying to figure out why I didn't answer.