When Tony attempts to open the secret passage, he hurts his left shoulder. Later, when Abby hugs him, it is his right shoulder he protects.
After Tony discovers the secret door in the wall, he removes the cigar from his mouth with his right hand. Immediately after in the wider shot, the cigar is in his left hand and a flashlight is in his right hand.
Throughout the investigation, Agent Cassidy's bandage thickness changes.
Gibbs asks Ziva to read the letter that is Arabic. As she is reading it the camera pans from let to right. Arabic is written and read from right to left so camera should have done the same which it did not.
When Tony and Agent Cassidy check out the building again once it's cleared if you notice very closely the "escape hatch" wall piece on the right used by the terrorist to escape the blast can be clearly seen standing out from the rest of the wall on the right.