For most of the Middle Ages the official position of Western canon law on the night flight was that it did not happen. The Canon Episcopi says that certain wicked women, turned back to the Devil, believe and profess that they ride out at night on beasts in the train of Diana, and that they are deluded. The passage goes on to say that these things happen only in the mind, that the Devil supplies the images while the sleeper's body stays where it is, and that anyone who believes such journeys are bodily real has lost the faith.
Two things follow from that, and they are worth separating. The canon is not friendly to the women it describes: it treats them as apostates deceived by the Devil, and it instructs bishops to expel sorcery from their dioceses. But the offence it identifies is a false belief, and the remedy it prescribes is correction rather than execution. The one thing it refuses to do is grant that the flight took place.
That refusal was binding for five centuries because of where the text ended up. It appears first in a handbook Regino of Prum compiled around 906 for bishops on visitation, passed from there into the collection of Burchard of Worms, and then into Gratian's Decretum in the twelfth century, which is where medieval canonists went to find the law. A rule reaching a court through Gratian carried real weight. Its own claimed origin at a fourth century council at Ancyra is spurious, and was already doubted by early modern scholars, but the misattribution only added to its standing.