When Tony goes to Ziva's apartment and meets Michael there, Michael has a several days growth of his beard. When Ziva looks at Michael in the morgue, he has a much lighter beard, making it look like he has recently shaved.
Before the team head to Israel, Vance has a red right eye but his eye is fine in Israel. When they return and Vance and Gibbs have their intense conversation, Vance's red eye is visible again in some shots. His eye is also red in the DVD interview with the cast. Clearly, the scenes have been shot out of sequence.
In the interrogation room Tony complains to Director David that he digs hanging out in concrete bunkers, "especially after 12 hour plane rides". The plane Tony flew in on was a C-130 Hercules. Even if it flew non-stop and refueled in mid air a C-130 would take at least 17 hours to fly from DC to Tel Aviv, not 12.