Skype has a tendency to mark certain calls, missed calls, and voicemails as unread, after I've already seen them. Usually this is after restarting; it will go back and mark one or two of the most recent ones unread just so it can have something to flash at me. But sometimes this happens even when it's just running normally. (The same message is seldom, if ever, marked unread more than once extra. But I can't be sure it never happens.)
I'm using 64-bit Windows 10, but the same thing happened on a previous install of 32-bit Windows 8.