It's happened to me as well.  One of the shortcomings in this system.  I've alerted Civil Comments to it and my comments have been restored.  They agreed that nothing I'd written was uncivil.  It's a new idea and the ways of making it work properly are still being worked out.  Unfortunately there are, as always, those who abuse the commenting system.  Voting down comments simply because you disagree with them is abuse of this system in my opinion.

I'll also note that a few months back I responded to a comment I very strongly disagreed with.  The original comment, and hence my response, were removed.  The original comment was 100% civil.  The man followed the rules and used his actual name and his thoughts belonged on the board despite my disagreement with them. I posted a comment protesting that it had been removed and it went back up within an hour, so there is some monitoring going on.  My only advice is to keep letting Civil Comments know.  They are trying to make this work.