I don't think people were that... insane.
By that logic most days could be construed as evil whenever 13th came up or indeed any number.
No I am afraid it is a simple case of either "13 people at Jesus's table" or "In some years when there are 13 full moons instead of 12 making it awkward to calculate dates using roman numbers like the church used to resulting in errors and conflict."
Sometimes it has nothing to do with religion but plenty to do with superstition of a group of people.
I always thought it had to do with Friday, October 13, 1307, when King Phillip of France had the Knights Templar arrested and destroyed.