When Gibbs sets Holly's coffee cup down onto the table, it has a lid on it. When Holly picks it up almost immediately thereafter, the lid is missing.
While Holly is being held captive in one shot her blouse is off her left shoulder. In the following wider shot it is on her shoulder.
Tony was mad at Tim for not meeting him at the bar at the Air and Space Museum. There are no bars at any Smithsonian museum.
Tony says he waited three hours for Tim at the Air and Space Museum "last night." The museum is not open after work hours during the week.
Gibbs sets a cup of coffee down for Holly Snow, however the sound of the cup hitting the table is too high pitched for a full cup, either the cup was empty or the wrong foley was used. Similarly, the force with which the cup was set down in order to make that sound, would have caused coffee to splash out of the top of a full cup.