Below is the screenshot of negative rep on a question I was never part of. It is now deleted. I have never seen this question before. Still the reputation is not restored. Is this a reputation system bug?
Almost always, this is a post you edited before you had 2K that was deleted. You got the +2 for the suggested edit and when the post was deleted, you lost that rep.
You made a suggested edit to that post that was approved, awarding you 2 reputation.
The post was deleted, therefore you lost 2 reputation.