When Gibbs and McGee leave the morgue in chemical suits, Abby claims that he hasn't left isolation. This is wrong, these suits only protect the person inside from contamination from the outside. But as the breathing air is vented to the outside (otherwise the suit would be inflated by the decompressed breathing air) any airborne agent would leave the suit on this way as well.
When Tony is in isolation and having severe respiratory distress and struggling for each breath, they have him on oxygen via nasal cannula. He needs high flow oxygen and it can only be given by a non-rebreathing mask. This may be due to the pending conversation, however considering the amount of dyspnea and cyanosis (as mentioned by Ducky), there would be little option. He is also lying supine. He has been diagnosed with pneumonia, which is fluid infiltrate (sporadic fluid) in both lungs. Considering the amount of implied severity, he would need to sit up. Fluid is affected by gravity and seeks it's own level. Considering the potential amount of fluid, lying supine could potentially obstruct the bronchial tree. Most who experience this degree of severity are more comfortable sitting bolt upright.
When Tony and Kate are given prophylactic doses of streptomycin they are given pills. Streptomycin cannot be given orally. It is only available as an intramuscular injection.
Starting at 03:11- during the shower sequence Kate doesn't wash her hair.
Abby's screen shows scanning electron micrographs (SEMs) of the pathogen, which would not have been possible in the time frame involved. She could only have prepared slide for the light microscope. Moreover, she claims that they show genetic characteristics of the strain, which is not possible. (SEMs only show gross structural features.) This is supposedly shown by the different colouration on the suspect sample but SEMs are monochromatic. Any colours are artificially added to highlight details and do not represent biological features.
When Kate mentions James Bond, and DiNozzo lists the actors who have played him, he forgets Timothy Dalton. Tony is near death from the Black Death. It's understandable in his delerium that he'd forget an actor.
The X-ray of Tony taken in the isolation area has no sign of pneumonia, but it does show two breasts: obviously an x-ray of a woman.
When Gibbs raises his SigSauer P228 towards the microbiologist, the muzzle is visibly too narrow to be a real firearm. Obviously a movie prop.
Starting at 03:11- no one else from the office is in a shower stall.