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- Thomasin (until the end) couldnt be a witch by Puritan standards: she could recite The Lords Prayer which during the Salem Witch Trials was used as a way to disprove being a witch, since it was believed demons and the devil could not confess Gods sovereignty. She also confesses she loves Christ, another thing the devil and demons were believed incapable of doing.
- The twins also might not be true witches. They cant recite The Lords Prayer but one man on trial at Salem was unable to say The Lords Prayer and blamed the accusers, saying they must have afflicted him. Considering they dont do anything actively malevolent and are killed by one of Black Phillips witches rather than recruited like Thomasin, its possible to assume they simply were used by Black Phillip to infiltrate the family and then done away with when his goal was achieved.
- The family at first determines it was a wolf that took Samuel because of the tracks, but the audience knows it was the Witch because we see her with Samuel before killing him. Since it is implied several times that supernatural beings were disguising themselves to appear to the family (the rabbit, the Hot Witch, Black Phillip, and Caleb and Samuel), it's possible that the Witch glamoured herself into a wolf to kidnap Samuel - or Satan did it.
- Witches, as portrayed in the lore the film's Witch is based on, supposedly have sex with Satan and Thomasin references this when frightening Mercy by pretending she's the Witch of the Woods and claims to have had sex with the Devil. When Thomasin actually does sign her soul to Satan, he first demands that she fully undress and appears to inspect her naked adolescent body. It cuts to the next scene. Was Thomasin forced to have sex with the Devil offscreen?
- Considering how effective and unbeatable the Witch was on Thomasin's family, it's safe to assume that in the universe where this movie is set, many innocent people (perhaps just as many as in real life) get processed and burned at the stake in the name of religion, while the real witches go uninterrupted using their powers to deceive people and perform real witchcraft on their helpless victims. For all we know, they still might be out there, cloaking their existence in the modern era, taking in new members and leaving no survivors...