Plot hole: The director of CDC informs the cabinet that the biological weapon at hand is a "prion variant indigenous to the East Congo" and refers to it as a "strain". A prion is a protein, not a bacterium, so it cannot be indigenous to a certain place and cannot belong to any strain. More importantly, prion diseases are not known to be transmissible in an airborne fashion (Mad Cow and Kuru, also prion diseases, are transmitted by ingestion), which kinda takes the air out of the threat. However, the description of prion disease symptoms and the example of Creutzfeldt-Jakob disease as being caused by prions are accurate.
Continuity mistake: When president Taylor asks Olivia to be her acting Chief of Staff, Allison rests her head on her hand, with only her elbow on the couch. In the next shot, her arm is suddenly resting on the couch instead. There's a straight cut between the two shots, so she didn't have time to move. (00:10:55)