I noticed an odd change in my rep a bit ago and went to investigate the source - I figured if someone had downvoted one of my answers I would try to improve it.
I managed to track the change to a question that was deleted, but fortunately still in Google's cache. A user asked a question that wasn't clear and provided sample data but not the password for it. I left a comment to that effect with some general suggestions to solve the problem. Another comment was added after mine with futher advice on improving the question. Eventually it was flagged and closed as unclear, as asker never came back or made changes. Apparently it just got deleted, and for some reason that gave me -2 rep.
At the same time I discovered another question I actually answered (with no votes either way) had also been flagged, closed, and deleted. But I lost no rep for that. Further research turned up another case where I had both answered and commented (I think) that also had a rep loss I didn't notice at the time.
I could understand if a comment is specifically targeted and deleted by a moderator for reasons of content, etc. But it seems odd that one could be penalized for leaving a comment to try and assist on a question that ends up deleted. Is this normal operation, was the delete not done correctly, or is it a bug?
I dug around on SE Meta (whew, ~600 results using all relevant search terms) and found this Q&A which notes:
removed - Most often, the post was deleted (this could be any post you took action on, not necessarily a post you owned).
This seems to imply this is normal behavior, but that a penalty only applies to comments and not answers that are removed when a question is. Seems like a faulty system to me - penalty for flagging poor posts (can leave a comment) or trying to help improve a question that ends up not making it?
I'll acknowledge and would like to avoid anything along the lines of "it's only 2 points" or "it doesn't happen that often."