I have had this happen before, no you are not red flagged. What this means is that the computer flashed an alert to let the pharmacist know that you had already received this months normal allotment of those pills, so he had to do an override with the proper reason code, so you could get the additional amount you needed.
Pharmacy databases are regularly audited by the FDA and the DEA, so they have to have that information in there, to prove why you were getting those extra pills, so they don't think the pharmacy was letting someone get away with drug seeking behaviour. Basically he had to punch the stuff into the computer that your dose had been upped for awhile, so you were running out early.
If you were red flagged, they would not have let you have any pills earlier than normal, and wouldn't let you get another refill until the very day it was due, no earlier. The information would also have been reported to your local clinics and hospitals, so when you went to the emergency room that doc would have been warned as well, and would never have believed your explanation and given you any extra pills.
So you have nothing to worry about, and pharmacies do, occasionally run out of their supply of pills, and 48 to 72 hours is the normal time frame for their new shipment to come in so you can get the rest of them.
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