Plot hole: When the CIA detects that Matt is accessing sensitive information to track Frost, they trace Matt's location and find out that he is using a public computer in a cafe. We then see that Matt is viewing the same kind of software, files, etc. that the CIA views at their agency. There is simply no plausible way that a random public computer would have CIA software, or be able to access CIA data at all, regardless of Matt's clearance. The computer itself would have to be on a secure domain.
Plot hole: Just after Rita rescues Jeff, Diane's grave is seen close to where Jeff was buried alive. Even though Diane's been dead for several years, her make-shift grave site looks like it was freshly dug. There are no fallen leaves or other debris on top, no new vegetation (moss, grass, weeds, etc.) of any type growing on it, nor has the mound of dirt settled, shifted, or been affected by the weather.
Plot hole: The girl disappeared from the RV. The RV is a crime scene - it should have been taped off, finger printed, and searched for trace evidence with luminol and a forensic light source. There is no crime scene (forensic) unit present on the scene. However, the parents are sitting in the RV waiting for the cops to contact them about their missing child. (00:19:00 - 00:20:00)
Plot hole: The premise is that the back-story is a fabrication, including the five being placed together in the police line-up and in custody in order to get them to work together. But in the flashback of Keaton in the restaurant, it is Dave Kujan who takes Keaton in. It is inconceivable that Kujan would be complicit in the staging of the line-up (and doesn't fit with the plot). And if Verbal is inventing it, then Kujan is going to know it didn't happen. It doesn't make sense and undermines the plot.
Plot hole: When the doctors are discussing the condition of Bowman's mother, a newspaper headline on the wall displays the pictures of both Bowman and Frank Poole. These pictures are actually still shots of the two actors from an earlier conversation they had with HAL in the previous film. Since Discovery has been dormant for nine years, how did Earth manage to use these particular shots for the newspaper?
Plot hole: While Harrison Ford is taking a shower shortly after arriving at the hotel, the 'bad guys' kidnap his wife from the hotel room. How did they know she was the one who had picked up the wrong suitcase (which contains what they are after) at the airport? They could only have assumed that. And the suitcase they were after was in the room so why didn't they just take it?
Plot hole: Reggie finds Tex's body stretched out on the bedroom floor, his feet tied to the radiator next to the wall and his hands bound to the bed frame, suffocated with a plastic bag over his head. The bed is a twin-sized, wood frame that Tex, a tall, strong young man, could have pulled the end of it with his hands and arms close enough to his face to at least attempt to tear a hole in the plastic bag so he could breath. He was obviously conscious early on because he wrote the name "Dyle" in the dusty floor with his finger. Considering the floor is covered in dust, there's not even the slightest sign of a struggle to free himself. Instead he just neatly prints the name on the floor before he dies.
Plot hole: The beginning of the film takes place in 1973 right after the original Texas Chainsaw film ends. Right after the house is burned, one of the townspeople takes a baby who survived the fire who is Heather. The film then takes place in 2012 but Heather seems 20 years old and should be 39.
Plot hole: When the police chief asks Joe 'where's the briefcase they were telling me about?' Joe tells him to look in the back seat of the white BMW. There are a couple of problems with this. First, the police chief is looking for a case with a bomb in it, because he received a phone call from the guy who had his BMW stolen. Even if he knew about the money, which is unlikely, the police chief has no way of knowing that the case he is about to open is not a bomb, since no-one saw Marcone steal the case with the bomb in it. Yet he opens it without calling the bomb squad. Second, Joe saw Jimmy put the case with the bomb in the back seat, so why doesn't he warn the police chief about it? (01:35:00)
Plot hole: At the beginning there is an audio recording of Thomas talking to the police. He explicitly says 'They killed her! They Killed my sister, my mom!' or something to that effect and that Thomas was arrested for the rape and murder of his sister and he killed himself in custody. At the end, his sister is killed and the little epilogue says that the sister's body was found in her brother's arms and when their mother found out about the 'death of her children' she killed herself. That doesn't make sense logically. Thomas was alive when his mother was dead, according to the clip at the beginning.
Plot hole: When the girl looks at the photos of Martin and his father while on the business trip, Martin is seen with his father and while wearing his boarding school sweater. But Harriet says later that he wasn't sent to boarding school until after their father was killed. Therefore, the sweater would not have been a clue in the earlier part of the movie.
Plot hole: When Dylan enters the vampire Vargas's bedroom to interrogate him, Dylan frequently steps away from the door to let sunlight in to burn Vargas, so that Vargas will cooperate with the interrogation. Vargas is in his bed and could easily cover himself with his sheets to block the sunlight, but never does.
Plot hole: If the Bird-of-Prey went to warp speed right after the whales were beamed up the ship would have already been so far away from Earth it would have been on its way back towards the sun, yet minutes later the ship is shown leaving the Earth, still at warp speed.
Plot hole: The sergeant tells Stone that he only has to listen for a bell for an important communication coming through and will then alert the rest of Wildfire. Yet later, Dutton notices a message already printed out. So at a facility this important, the sergeant just ignores the machine if it prints out a message and doesn't ring? He has to have clearance to read them or they wouldn't print out where he is. It's a bit too convenient for the plot that he wouldn't visually check each message to make sure.
Plot hole: Early in the film, we learn that the former prostitute Annie Crook is married to and has an infant daughter (Alice) with Prince Edward Albert Victor. Secretly outraged, Queen Victoria dispatches various high-ranking operatives to eliminate this potential royal scandal. To that end, Prince Edward Albert Victor is secreted away, and his wife Annie Crook is kidnapped and barbarically lobotomized. We then learn that he baby, Alice (who was fortunately in the care of two other prostitutes at the time of the kidnapping), was sent to live with the parents of Annie Crook, no doubt saving the baby's life. That is the last time we hear of baby Alice until near the end of the film, where we are puzzled to learn that Alice was not sent to live with her grandparents at all, as stated earlier. Rather, the prostitute Mary Kelly took baby Alice away from an orphanage to raise as her own. No explanation is offered for this discrepancy.