It’s easy to flag submissions by accident and I’ve definitely done that and had to unflag them. I flag submissions on purpose fairly often when I feel they are really poor quality, spam, or way off-topic for HN. I also flag submissions where the discussion has gone off the rails.
Flagging a comment takes extra work because you have to click through to the comment. I’ve never done that by accident and tried to only do it for comments that violate guidelines. Sometimes I subjectively feel a comment is trolling and will flag it. That’s not strictly against the guidelines and is a judgement call.
(The worst is when I accidentally hide a story. That’s way too easy to do and too hard to undo.)