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While looking at someone else's reputation history recently I noticed the following anomaly -- the total for one day was +100, which is not the sum of the total activity for the day (+50 and +40). Since the day in question was a long time ago, I doubt that it's because of some pending action that hasn't been fully processed yet, nor do I think it's from a deleted post -- this particular user has made very few of them.
In short, it looks like simply a bug.

Screenshot of User John B's Reputation History

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Got a link for us? – Bart Feb 5 '13 at 20:06
Since you're looking at rep from 2008, the most likely cause is a deleted post that received an upvote that day. You get to keep rep from deleted posts if the post is over a specific age when it gets deleted (I think it's posts over 60 days old, but am not sure). Also @Bart, here you go – Rachel Feb 5 '13 at 20:18
@Rachel: If he kept the reputation from it being deleted, it would still be present in the history, as is the "What is the single most..." post, which is currently deleted. – animuson Feb 5 '13 at 20:21
@animuson You're right, I forgot deleted posts do show up in rep history :) Perhaps it was something hard-deleted, like the boat question? – Rachel Feb 5 '13 at 20:39

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