OK, so you are saying that on June 16, the doctor told you that you were 11 weeks 3 days along? And that's puzzling because it does not count back to April 14?
Here is what I'd do. I would go to the next appointment, and explain that when you were at the E.R., they gave you a gestational age figure that doesn't make sense, and ask for another ultrasound that very day. By now it's going to be pretty late for precision, unfortunately, but it should be able to tell the difference between two guys a month apart with a period in between.
I assume you know that the gestational-age count (the figure in weeks) begins on the first day of your last period before getting pregnant? Because you had a pretty clear period after having sex with your ex, and because if the ER doc was implying the pregnancy is from before your last period (but if that was right, he should have told you that you were 13 weeks 1 day, which he didn't), in your shoes I would assume that the ER doc got the count wrong and you are pregnant from the second guy, after your last period. But do get the ultrasound, and see what results your doctor gives you. And write back. :)