When Sarah arrives at McGee's apartment, it is 2:30 am. When McGee is standing outside the bathroom door while she showers, and the conversation they have after she gets out of the shower, there is sunlight streaming through the bedroom and living room windows (you can see the square of light from the window next to McGee on the wall in the bedroom.) Then, while doing the time line, the room is dark again.
In the scene where Special Agent Gibbs is interviewing the female college student in her dorm room, the young woman shows Gibbs a picture of her boyfriend in Bahrain. The picture shows a sailor, in uniform, in front of a mosque. Military members are not allowed to go off base in their uniforms in Bahrain and there are no mosques on the base.