This really is minor, and inconsequential, but it's a bug nonetheless.
Anyway, here it is.
Find a new user with 1 rep that has asked a question. Downvote question. Remove downvote. Voilà, 3 rep.
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Yeah, this has been known for a while... I don't think anyone is too concerned, given that it only works for users without any reputation, and it doesn't really give them much.
These inconsistencies will no longer happen. As part of some large reputation changes, downvote reversals will restore the correct amount of reputation (including adjusting for the reputation cap).