I encountered this twice as of late.
Up top with the notifications, where it tells you You Have # New Messages
At one point it only stated one, but at the time I had two which were entirely new that day and I did not check my box any time prior.
And another instance it said I had one, but I got two from the same user. So one beforehand didn't register in the notifications?
Sorry if any of this is confusing. >_>
And I am speaking more of site notifications than email ones.