I have notice two issues with the reputation graph:
1: This user has a higher score on the graph than in reality
I happened to notice this user profile where the user's graph reputation does not match their actual reputation. The person in question was hit by a -100 penalty for an offensive answer a while back, but the graph doesn't reflect that. I thought it just didn't update when I noticed this at the time, but the person has since gained and lost reputation and at all times the graph was +100 of their actual reputation. It seems, based on Shadow Wizard's comment that this is because the reputation change is non-public. OK, fair enough...
This old question, which was marked as status-completed, noticed a similar phenomenon for placed DVs. This prompted me to examine graphs more carefully. It seems that this hidden -1 has been updated, as I checked several users and did not find any others that had lower actual reputation than graph reputation, so . (Since the number of DVs placed is public, I can be reasonable sure that these users have placed -1 rep DVs, although strictly speaking they could be 100% question DVs.)
2: Some users have a lower score on the graph than in reality
I did, however, find many users where the graph says their reputation is much lower than it actually is. Perhaps that is from deleted downvotes turning into hidden +1s, but those should be balanced by hidden -1s, so its not clear what happened. Seems there is some error in the logic - maybe the -1s do affect the graph now as per the status-completed, but the corresponding +1s don't? Whatever the case, I can't imagine it is intentional.
Edit: I went back to find some examples today & didn't find any. I think the issue has been resolved - either it was a caching issue or a change was made to the code after this post.