I believe it has something to do with the 3-day window for providing the summary to the patient.
I was able to reproduce the issue:
If you see a patient, and during the visit print them the summary/CCD you can look at the MU status (top right button) and it will show you the passing grade for Core 13... until 12:00am that night. If you leave the unfinished note in your inbox, and go to finish it the next calendar day, the status will show incomplete Core 13, unless you "print" one again... in which case you'll then get credit, but that credit will be applied to the date it was signed, whereas the rest of the Cores are applied to the date of the visit.
If you finish notes after midnight, then run a MU Wizard report for just that date (the date of 12:01 am), you'll have a numerator of however many notes you signed (if you "re-printed" the summary as above), but a denominator of zero (until you see more patients, or more precisely "sign chart notes", that date).
