In a scene where Mercy is fighting Thomasin, her bonnet comes loose from her head. However, in the next shot, the bonnet is pinned back.
When Thomasin is milking a goat in the barn, there are several quick cuts between her and Mercy. Each time we cut to Thomasin, her goat is positioned at slightly different angles.
One mistake in the dialogue is the incorrect usage of the personal pronouns "Thou" and "You." During the 17th century, "You" was reserved for formal situations, and when one was addressing someone of higher status/rank. "Thou," on the other hand, was used in personal/informal settings and between peers and close relations (similar to the French Tu vs. Vous). Throughout the film, the characters use thou and you interchangeably; however, a close-knit family such as theirs would not have likely addressed each other with the formal "You."
The very poor family is shown lighting their home using multiple candles. Candles were extremely expensive to make; a family at this level would have used rush lights, not candles.
Near the end, when Thomasin is seen with her mother, her blood-stained dress top is closed with buttons or snaps. Shortly afterwards, when she removes the same bloody garment, she does so by untying multiple string ties.
This is not a goof. Thomasin was wearing a sweater or some outer garment that had buttons over her blouse that had strings. You can see her placing the sweater onto the ground just after she walks through the door. You can see the difference between the two because the sweater has straight sleeves whereas the blouse has puffy sleeves.
During Caleb's burial scene, the clouds and the smoke rising from the cabin don't move.
The wood in William's woodpile appears to have been cut with either a mechanical saw or with a two-person saw. There is no one to help him operate the two-person saw as his children and wife do not appear physically able accomplish this task.
The metal spring leg-hold trap the father uses to try to catch a wolf wasn't invented until the 1800s. Before that trapping was done with snares and other types of traps.
The nails holding the chicken house together have modern round heads. Seventeenth-century cut nails would have rectangular heads.
(01:23:15) As she's imploring Black Philip Daniel Malik to talk to her, the audio is half a beat behind her mouth movements.
Boom mic is visibly hovering over the mother when she is praying in bed and Thomasin peeks through her bed curtains.