Plot hole: The whole concept of a kidnapper 'pretending' his victim didn't get on the plane in the first place is utterly laughable. Even if nobody saw her in her seat, why didn't they see her walking down the aisle to her seat, or waiting to board the plane, or in the boarding tunnel itself? Why isn't she listed on the passenger manifest, or on her mother's travel documents or airline ticket? And there would have been security cameras all over the airport.
Plot hole: In the end, when Charlie is advancing on Emily while turning his light on and off, the final time he turns it on, Kathrine is in front of Emily. How could she get there so fast without being heard? There's at least 4-5 inches of water that would make sneaking very hard.
Plot hole: In the course of the story it's said that at the time the black hole went out of control, it had a mass of "half a mountaintop of granite." But in a flashback scene Dr. Krone is shown growing the mass of the hole by feeding it large numbers of lead bricks in the laboratory. It's a little hard to believe his lab could store, or even afford, enough lead bricks to equal that much mass.
Plot hole: At the start of the gun fight at the house, a snowball is thrown at Jack who then follows the person into the street. When they turn around the person is wearing a hockey mask and Jack realises he's in trouble. Jack would've seen the person wearing the hockey mask when the snowball was thrown, as the person had to be facing him to throw it. There was no reason after that for Jack to follow him.