When the flatbed with the container leaves the docks, there are two short shots when we see the left/driver's side of the container and it is undamaged. Later, Jack stops and looks into a tear in the container, more than a meter long.
Landry from the CDC says that the pathogen is a modified version of the Creutzfeldt-Jakob disease (CJD) prion that kills with a day or two. That is not possible, even with a modified version, because pathogenic prions cause normal brain prions to malform, causing slow degeneration of the brain. Moreover, prions are proteins, so they are not volatile and cannot be weaponised as a gas or aerosol. They can only infect by ingestion (e.g., eating infected meat) or by injection, not by inhalation.
The front of containment truck transporting Bauer has the word 'HAZMAT' emblazoned reversed as 'TAMZAH', so it can be recognised in vehicles' rear-view mirrors. However, the letter 'Z' is not reversed.
By using infrared scanning for the building Seaton claimed the biological weapons were stored, the FBI would've have avoided a confrontation with Seaton and his men.
When Greg Seaton gives FBI the coordinates for the location of the weapons he says: "32 40 4 POINT 23 NORTH. 11 7 10 POINT 42 WEST". The literal interpretation of this would be 32°40'4.23"N 11°7'10.42"W, a position in the Atlantic Ocean, just off the coast of Morocco where no warehouse could possibly be. On FBI's screen it shows that they interpreted what he said as 32°40'4.23"N 117°10'42"W, but those coordinates are in the Pacific Ocean just outside San Diego, California, while their satellite photo clearly show a warehouse on land.