It's commonly caused by deleted questions/answers whose up/downvote did affect your reputation. They get recalculated correctly in
/reputation and the API, but for the user rep (as shown in flair) it only happens for the day of today and for rep graph it don't happen at all. At least, that's my observation.
If you request the moderator for a recalc, then the reputation as shown in flair will match the one as shown in
/reputation. You can request it by flagging an arbitrary post of yourself or leaving a mail at team@stackoverflow.
Related: Rep graph not accurate, there are apparently different algorithms/caches for reputation