We see the box being buried in concrete, yet when the box is being dug up it is just buried under earth.
In the 1958 scenes, the box is shown variously as painted and unpainted. In a time-lapse scene, we see the box age from unpainted raw wood to dark and moldy, but when it is being buried, it is already dark.
In the beginning of the movie, they say Tommy Jr. went missing 8 years ago and at the end of the movie, they say 10 years ago. Based on several other events happening in the movie, it didn't take 2 years to investigate the case.
Throughout the investigation, they refer to the events happening in the spring of 1958 but on the wife's tombstone, they have her death listed as Nov 1958. All the events happened AFTER her death.
When Matt goes to the diner later in the movie, Sally Ann is putting coffee pots on the warming plates. The coffee pots are the modern kind with brown top for regular, and an orange top for decaf. In 1958, most coffee pots would have been metal. And decaf if available was served in little orange packets called SANKA.
The highways the Rambler drives on have the wrong color striping. In 1958, the shoulder stripes were yellow and the centerlines were white. Modern embedded road reflectors can also be seen in some shots.
Throughout the 1958 scenes--including his wife's graveside where the headstone says Nov 1958, Matthew Wakefield is driving a 1959 Rambler. A '59 could conceivably have been on the road in late '58 but not owned by a man with no job and losing his house. It was also in pretty rough shape for a brand new car.
As John and Matt drive down the town's main street, one of the storefronts they pass has one of the modern "OPEN" neon sign in the window.
The 1958 white rail fence is modern prefabricated material. The screws and tabs holding the sections together are visible.