I haven't had this happen to me, but know of others who have and if you were dating from your last period, it can be difficult to know exactly when you ovulated and when the egg was fertilised and embedded, so sometimes the pregnancy is earlier on than you think, or than the dates show. They use the later scan (12 weeks) to accurately date your due date, so the sonographer is giving an estimate from the size of the foetus etc.
Either way, congratulations!!! Wishing you a happy, healthy pregnancy and birth!