According to Goodwife Cruff, Kit is the cause of the becalmed ship.  She and her husband have made Kit quite aware that "they (consider) the becalmed ship all her doing".  Goodwife Cruff thinks that Kit is a witch (Chapter 2).

In the previous Chapter, Goodwife Cruff's young daughter Prudence had accidentally dropped her doll, a precious gift from her Grandpa, overboard into the water.  The child was devastated, and Kit, meaning to be kind, had impetuously leapt into the sea to fetch it.  To Kit, her action was nothing special, because in the tropical island of Barbados, her home until now, the water is warm, and everyone knows how to swim.  In Puritan Connecticut Colony, however, the people are not at all at home in the water to say the least.  Anyone who can swim is regarded with suspicion, and there are some, like narrow-minded Goodwife Cruff, who believe that "no respectable woman could keep afloat in the water"; any woman who can must be a witch.  Goodwife Cruff's belief stems from the infamous "water trial", a test given to women accused of witchcraft - "a true witch will always float...the innocent ones just sink like a stone" (Chapter 1).

Goodwife Cruff already thinks Kit is a witch because of the incident concerning her daughter's lost doll, so when the ship is becalmed, she suspects that Kit is sabotaging their journey with even more witchcraft.