Our system works well to sort out comments that shouldn't be published, but sometimes things slip through the cracks. That's what the flag is for! Flagging a comment notifies staff, so before you flag a comment, make sure you've considered it for a moment--you should only flag comments if they contain abuse or harassment, spam, threats, or if the username and/or avatar is offensive. Once you've determined that a comment does indeed merit a staff notification, you can click the flag button in the lower lefthand corner of the comment in question, and select the reason for flagging. Keep in mind that flagging comments without valid reason will have a negative impact on your trust rating, and if you continue to do so, over time, your flags will cease to count.
One common misconception about flags and likes is that they affect your voting behavior. The only thing that CivilBot looks at when assessing your voting behavior is the civility rating that you give to comments in the comment rating process--flags, reactions and quality ratings are viewed separately.