When all the other characters look at "Sam" and "Gary," they look up at Sam and down at Gary, looking at the actors, not at where the person's face whose body they're in would be.
In the opening scene the amount of liquid in Sam's banana daiquiri goes up and down throughout the shots.
After the final battle when Nora and Gary return home, there is no mention of Trevor who is lying dead on the floor.
At the diner, Dean hands a fork to Sam who then puts it in his mouth with the tines facing down. In the following shot a second later, they are facing up.
When Sam/Gary is standing in front of Gary's mirror, the Gary actor is obviously behind a screen since the reflection doesn't quite match the movements of Sam/Gary.
When Dean is listening to Sam's messages in the voice mail, he should hear Gary's voice and not Sam's, since Sam was trapped in Gary's body and hence used Gary's vocal cords.