This morning my rep was 315. I downvoted an answer (and left a comment explaining why I thought it was a bad answer) which took me to 314.
When I next visited the site, I got a green +1 icon telling me my rep had increased. Clicking on my rep history, it says my last increase was +2 for an edit a few days ago. I was on 314 and I've got +2, that should be 316... but I was on 315.
What's happened is that the answer that I down voted has been deleted so I've got my 1 back, but the 1 point deduction/reimbursement for downvoting does not appear anywhere in the rep history.
It took me a while to figure this out.
Is this a bug? Or am I fundamentally misunderstanding how it works?