Yes, they can tell the difference between an 11th-week pregnancy and an 8th-week pregnancy. The embryos look very different.
There would be a difference and they would know it from the ultrasound if the baby was 11 weeks versus 8 weeks on the ultrasound right?!?
No, you have nothing to worry about. You had a normal period and it's been confirmed by ultrasound in the early stages of pregnancy. Your pregnancy has nothing to do with the guy on September 6.
ps -- Since the sex September 6 was obviously unprotected (or you would not have wondered) don't forget to check for std's in one of your prenatal visits.