After Abby is pulled from the car, Gibbs' hand goes from on her shoulder to over her ear and back again as the camera switches angles.
Lt Seabrook is supposed to have died of carbon monoxide poisoning. Her skin is seen as gray and pasty. Carbon monoxide causes the victims skin to turn bright pink, not gray.
When Ziva is researching Y pestis, the picture she enlarges on the search site shows a strain with blue tips. The strain with blue tips is the one that Tony got sick from. A picture of a normal strain wouldn't have the blue tips.
If Lt Seabrook died from carbon monoxide from the vehicle's exhaust. OTTO, the vehicle, runs on unleaded modern fuel with a catalytic converter. It would take days, if at all, to die. At worst the victim would get dizzy, which Abby does.
There would have to be ducting between the exhaust and cabin air vents. This was never investigated for clues.
In an ultra-sophisticated high tech computer system run by AI, the malicious software discovered is displayed in a series of "if - then" sequences in computer BASIC, dating back to the age of the Commodore 64.
There is very little carbon monoxide in the exhaust gasses generated by a properly tuned gasoline engine. Most of the exhaust is carbon dioxide and water vapor. But if those gasses were to be recirculated several times through an engine then a deadly concentration of carbon monoxide could be formed.
When Otto malfunctions, Roni is shown trying to reach the kill switch over the steering wheel. It appears to be very far away, and she can't reach because of the tight seat belt. Dr. Engler tells Tony all she would have had to do was push the kill switch "right in front of her on the dash." The switch was not right in front of her, nor did it appear to be on dash.