When at the bar with Elliot the straw in JD's drink appears and disappears.
After Elliot dumps the beer on herself the glass alternates between being completely empty and having some beer left in the bottom between takes.
The janitor doesn't have a wolf he has a Siberian husky, although it is part of the wolf genus.
When Dr.Turk is showing the interns where he is going to cut Prv. Dancer during surgery, he draws the line on the left side of the patient's body but in the next shot the line is on the right side.
When Dr Cox draws blood from JD there's no tourniquet on his arm. Venous blood doesn't have the back pressure to be drawn without collapsing the vein when a tourniquet is not used.