From Redditor u/Madlyneedahouse:
When the first baby is killed, the baby is ground up and rubbed over the witch's body. We then see her rubbing a long stick down with the same blood. It was believed at the time that witches used blood to give them the power of flight.
After Thomasin wakes up at the end of the film, and the twins are nowhere to be found, she goes into the woods where she finds a circle of women dancing around a bonfire. All of them are covered in blood. They then begin to levitate.
Thomasin, who hasn't touched the blood of her siblings is, however, covered in her mother's blood.
From Redditor u/Rennim:
The Witch probably took them and left Thomasin. All the other occurrences with the Witch were likely to frame Thomasin, and this was the last.