In The Witch, William himself buried Katherine alive.
She sleeps beside him with blood dripping from her breast and he wakes up without any surprise.
Why is William unaware of Katherine being alive, after burying her?
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He did not bury her alive.
The mother was mourning the death of her young child and she could not let go of the child.
I understand your confusion, but here's what happened.
And the movie continues (screenshot #2)