(at around 1h 20 mins) A square hole is cut in the apartment ceiling to fix a pipe causing a leak. There is a shot from inside the ceiling, looking down to the floor past the pipe and through the square hole. Dahlia enters the room looking up at the newly repaired pipe. She is obviously barefoot. She hears a noise and we cut to a shot looking down a hallway where there are wet footprints and someone hurriedly clearing the hallway to turn right out of shot. Curious, Dahlia immediately follows the noise. She is now making shoe-noises as she walks and as she climbs some stairs we see she is now wearing laced-up running shoes when just a second before she was barefoot.
(at around 31 mins) After Dahlia dumps out the first bucket of water that has dripped from the ceiling, the sink is flooded with dark water. The next shot showing the sink has drops of clean water, and no dark water residue anywhere in sight. The water in the sink had not been turned on yet, so there should not have been any clean water in it.
(at around 1h 30 mins) Near the end of the film, Kyle is carrying a clear plastic container of Ceci's dolls when he enters the elevator. You can see a sock puppet and a pink sheep on the outermost side of the box. When the elevator doors open at the first floor, the contents of the box have changed.
(at around 1h 30 mins) Near the end of the movie, a paramedic is heard giving Dahlia's age as 30. However, in the opening scene, Dahlia is seen as a girl of at least five or six in 1974. Thirty-one years later in 2005, she'd be at least 36.
(at around 18 mins) In the custody office when Dahlia is arguing with Kyle over hers and Ceci's relocation, Dahlia takes out a newspaper cutting detailing how good the school near her new apartment is; she holds it up with her right hand. In the following shot the article has switched hands, and Kyle snatches it from her left hand.
About 15 minutes, Ceci goes up the stairs of the apartment building to the roof. The parapet wall (where she picks up a backpack) is clearly much less than 42". This height is (a strictly enforced) New York City Building Code.