When John throws the football back at Mark's friend, Sarah is just getting her camera out and doesn't take pictures of John until after he throws the football. However, when John is looking at her website later, there is a sequence of photos of him throwing the football.
When John and Nicole are making out in the water (about 5 feet deep) at the beginning of the movie they are far away from the other people at the beach party. When John's leg starts glowing she has to swim to shore and then run to the other people. But in the video from the website they are in shallow water (2-3 feet deep) and the person filming them is apparently quite close as the video is very clear and close up.
When the Mog is lifting John up by the throat with his hand, his thumb and forefinger are resting on John's jaw. When John speaks to him, the Mog's hand is suddenly much lower, but in the subsequent shot the hand is back in its original place.
The bulk of the movie takes places in Paradise, Ohio. However, the law enforcement officers, referred to as Sheriff (and one assumes deputy), are not dressed as Sheriffs and Deputies in the State of Ohio, who wear a black top with gray pants. Also, Sheriff's vehicles in Ohio are all black.
John is not human, but Loric, so the way things work in his body may not be the same as a human, so the scars on his legs could theoretically stay the same. Also, scars are not guaranteed to shrink as one ages, so as he grows and his skin stretches, it would make sense that the scar would grow and stretch in a similar manner, especially if the scar is burned into his skin in a size relative to the size of his leg at the time.
When Henri gives John his phone, he informs him that he'll be calling every hour John is on his own to make sure he's okay, and if John doesn't pick up, Henri will know something is wrong (implying he'll assume the Mogs have attacked John and will come looking for him). During dinner at Sarah's, John reluctantly surrenders his phone after noticing three missed calls from Henri. Despite the fact that John had not answered his phone for three hours, Henri did nothing about it, and does not even mention it at all afterward.
When returning to Paradise, Ohio from Warsaw, Indiana, John and Sam stop by a rail track to assist Henry, and an AVR (Allegheny Valley Railroad) train passes them. The AVR services Pennsylvania (which is where the movie was shot) but has no trackage or trains serving anywhere between Paradise, Ohio (just south of Youngstown) and Warsaw, Indiana (west of Fort Wayne).
The goof items below may give away important plot points.
When the Beagle starts to transform in Sam's dad's truck, the truck is shown sinking to the ground and the rims bending. Part of the truck's frame is shown as being torn. Yet in the graveyard the truck looks as if none of the damage happened at all and still looks shiny as it did in Sam's garage.
Immediately before John makes his parkour-esque run through the forest, the beagle is seen whimpering on the bed. When he finishes his trip, off the cliff and onto the rock next to the creek, the dog appears whimpering over the edge of the cliff. A beagle could not have possibly been able to keep up with the incredible speed of John. But as is shown later the beagle isn't really a beagle so it could run a lot faster than a real one or transform into something else during the run.