When the Ones We Don't Speak Of first raid the village and Kitty takes the children to the cellar, there is a quick shot of Ivy at the door as Kitty begs her to close it and hide with them. A boom is just barely visible lifting out of the frame on the right side of the frame.
When Alice is explaining to Lucius what happened to his father she says his body was found two days later floating in the river. In the voiceover towards the end of the movie she said his body was found three days later.
After Ivy falls in the hole she puts the things she is carrying very near the hole, at the edge. When she is climbing out, the things have disappeared from the edge, and once she is out, they are a few meters from the hole.
As Ivy listens to Mrs. Clack ask the villagers to offer Lucius their prayers, Ivy is standing at a distance from the crowd. In the next shot she is standing much closer and is now slightly behind them.
When Ivy finds Lucius stabbed, she hugs him until she is taken away by her father. We see there is nothing on her shirt when she leaves. In the next scene her shirt is smeared with blood down the front and on the sleeves.
During the wedding feast, two villagers throw a carcass onto a stone slab at the edge of the village as an offering to "those we do not speak of". The carcass appears topside-down after it is thrown. However, when viewed from the other direction in the next shot, the carcass is topside-up.
When Ivy enters the woods to get help for Lucius, off in the distance through the trees you can see a pole with a bell on it, used by the villagers for warning purposes. This has been mistaken for a telephone pole and the bell as a transformer.
The goof items below may give away important plot points.
During the voice-over segment beginning at approximately 1:30:20, when August Nicholson (Brendan Gleeson) tells the story of his brother's murder in the emergency room while attending a drug addict, he says that while attempting to dress the wound (approx 1:31:28) to the addict's ribs, the addict pulled a gun from his jacket and shot his brother. To examine and then dress a wound to the ribs, the brother would have in all likelihood removed the addict's jacket (as well as a shirt we can assume) and laid them aside, again, in all likelihood, out of arm's reach of the addict so he would not have been able to pull a gun from his jacket.
After Noah falls in the hole in the woods he is on his back and appears to die while staring at the top of the hole. In the next shot his body is lying sideways in the hole and he is staring to the side.
When Ivy emerges from the woods and the Land Rover pulls up, we see a view of the side of the truck where it says it's from the Walker Wildlife Refuge. The car is so clean and shiny that you can plainly see the reflection of the camera, dolly, tracks, feet, and a wall.