On two recent occasions I have flagged a post for moderator attention and then lost a single rep point each time.
I did flag a post again today, and the same thing happened. Is this supposed to happen, or could there possibly be a bug?
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No, normally you don't. I flagged this post, as well as a random post on Stack Overflow, and neither has resulted in a -1 penalty. This applies to all 3 kinds of flags.
Were you flagging posts that you had just downvoted? Remember that downvoting costs 1 reputation, and if I'm not mistaken it's the only way to lose so small an increment.