There have been a few bugs with the Rep graph on the user profile page that cause it to display a different value than the actual Rep for the user...
The +100 Rep bonus from associating accounts across sites does not appear on the Rep graph, making it display 100 less than the true user Rep.
There was a bug I previously posted on uservoice having to do with offensive penalties. From the UV post:
I recently noticed a user (#82118) who made a joke that was not very well received and got hit with a -100 penalty for offensiveness. They had already earned around 100 points from upvotes for it.
When I looked at their reputation tracker on their profile, I noticed that the graph didn't agree with their reputation (the graph was much lower). Also, the list next to the graph showed "0" and "-100" next to the offending answer, instead of "100-ish" and "-100".
It appears that the reputation tracker takes away all points earned AND subtracts 100, even though this is not what happens to the actual user reputation. The result is that the reputation tracker is below the actual reputation.