At least that is what they did with me. With my first OE cycle they transferred four embryos in one catheter. I actually watched them on the screen and could see the four little dots get sucked up into the tube from their dish and then inserted leaving the tube.
I'm not sure why he left and came back. It is possible that other clinics do it differently and they had them in different catheters. If you are concerned you could call your RE and ask them what happened.