An important thing to note about the story is that since a belief in witchcraft was pervasive at the time, any unexplained phenomenon could be attributed to black magic. Some examples of the things blamed on witchcraft included illness and mysterious death, as well as this "thing worthy of observation" where we find the only place that a library is mentioned in the book (this was long before Ben Franklin, so it is a private library).
Winthrop the younger had in his library a volume in which the Greek Testament, the Psalms, and the Common Prayer were bound together, and that he "found the Common Prayer eaten with mice, every leaf of it, and not any of the two other touched, nor any other of his books, though they were about a thousand."Sounds like witchcraft to me. Of course, it also sounds like hearsay, which comprised much of the evidence at the Salem witch trials.