Plot hole: When Kim sees Gary she runs into the master bedroom, hides her bags, goes into the closet and up to the attic - all in the time it takes Gary to run five yards to the bedroom door. And considering how much noise the attic door made he should have heard her. Plus, how did she manage to get the door hatch closed when she had gone up?
Plot hole: Dina Araz was executed at 8:57pmin the previous episode. At 9:01pm during this episode, the terrorists have already placed her body in the van, driven off with it, and abandoned it. Then someone had found the body, reported it in, and the information gotten to CTU. All in the course of four minutes. That is impossible, no matter how fast the terrorists were.
Plot hole: When Kim is brought back to the police station for the last time, the officer explains to her that they now know it was Gary Matheson who killed his wife, and that they are still looking for him. Why then, would Kim and her police escort not even consider the possibility that he might be hiding at his home when they arrive to get Kim's belongings? Even if the police searched the house once before, you would have to be insane to allow a teenage girl to enter the home of a known murderer on the loose. Beyond that, Kim herself never seemed to consider the threat.
Plot hole: At 01:50 am, Chloe is told to go to Sabir's house. She arrives there approximately 5 minutes later, at 01:55:45. At 01:58, Jack is told that the closest tactical team is 15 minutes away from Sabir's residence. A few moments later, Jack mentions that the tactical team is 10 minutes apart from Chloe, meaning they bothered to send the team over there even though any officer currently at CTU HQ, including Jack, could get over there a lot sooner.
Plot hole: Martha Logan told Evelyn about the transcript and hid it in her bra in front of her. Yet when Mrs. Logan later tells her husband about it Evelyn doesn't seem to have any idea what she is talking about. While it can be considered a character choice for Evelyn not to speak up, there is no reason at all why Martha, who is so desperate for her husband to believe her, doesn't ask Evelyn to verify it.
Plot hole: Day 8: Renee mentions that after her previous sting operation with the FBI against Vladimir Laitanan, he had major facial reconstruction surgery, but in all of the photographs of said operation she shows CTU New York, Vladimir looks exactly the same as he does now.
Plot hole: Jack is informed that experimental treatment using stem cells from a genetically compatible donor is being developed that might be able to cure his condition. Stem cells are used to treat diseases where a cell type in the patient's body malfunctions, such as insulin-producing beta cells in diabetes, or where injury has killed cells that do not regenerate, such as in spinal cord injury. In these cases stem cells can replace the damaged cells and make sense as therapy (bone marrow transplant as leukemia treatment is one real such treatment). Prions (which is what the show calls the bioagent) and bacteria (which is how the show describes the bioagent) cannot be cured by stem cells, since the cause of the disease is not damaged or defective cells. Even if the disease damaged brain cells and stem cells cured that, it would resume later since the causative agent is still there.
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.
Plot hole: In the scene when Jack and Nicole isolate the Singers, Jack is informed that they've been tested on site, and the results were negative for the virus, less than 15 minutes after being isolated. However, later in the day the results take several hours to be made available, and have to be processed elsewhere, in a lab. (00:17:45)
Plot hole: The head scientist tells Tony that they need Jack's organs to reconstitute that pathogen since there is not enough of it in the sample. Assuming it's a virus, even a small sample could easily be grown in the lab to yield large amounts of the virus. Assuming it's a prion, they don't even need a sample since the could simply build it again from scratch so long as they knew the protein sequence (which is a likely assumption). In either case, Jack is unnecessary.