When JD asks Elliot to put her phone in Dr. Cox's pocket, you can see her slip it in his left pocket. Later, as he is sitting at his desk, he hears JD talking and grabs the phone from his right pocket.
Carla told Turk she's only been pregnant for two weeks. However, at two weeks, one would not test positive for a pregnancy test yet because it would be too early for HCG hormones (what a p-test detects) to be prominent enough in her body.
When Ted is talking to Turk about Gooch he says that Gooch is his first girlfriend. However in seasons before this he has mentioned many times that he was once married. In particular when he tells Dr. Cox and Jordan that they are still married because he mixed up their divorce papers with his own.