Goofs

As Ziva returns her concert ticket to Abby, Abby's left wristband is missing and she is scratching her wrist as if the skin is irritated.

Ducky asks Tony to perform a blood count by adding Methylene Blue to a blood drop on a slide. A blood count can never be done this way, and this would be useless for identifying hemorrhagic fever. Methylene blue isn't for blood counts, it's for identifying and treating methemoglobinemia, which is a rare blood disorder, not a virus. A blood smear stained with Methylene Blue would never look like it does in this scene - rather than a smokey blue color, this slide has been stained with hematoxylin and eosin.

You can't get Top Secret clearance without knowing the consequences of revealing secrets to people without clearance. There was no need for a NDA.

When the commander is 'reading in' the Director, the cover sheet shown in the briefcase is the standard blue Confidential cover sheet. Confidential is the lowest level of classified US material. The levels are Unclassified (green), Confidential (blue), Secret (red), and Top Secret (orange).