The Flagellants were called heretics because they wandered around preaching weird things, like that their group’s own flails and cords were essential to salvation, and that they were the only group that counted, blah blah blah. I don’t remember the details. Totally disregarding and disobeying all authorities but their own leaders and whipping up mobs to kill Jews were part of the movement also, if I remember correctly, but I could be remembering other iffy groups that got in trouble for good reason.
Mortification is just supposed to be part of a well-balanced spiritual exercise routine or training regimen of asceticism, fasting, alms, and prayer, substituting a controlled system of discomfort or minor pain for the traditional outdoors rigors of wilderness heat or cold that were used as training by early Christian hermits and monks, or for the continual persecution and annoyance suffered by early Christian martyrs and confessors.
The problem is twofold. First, the difficulty of getting a spiritual director with good judgment, and of controlling people who use mortification, so that they were not getting hurt or aroused (ew!) or discouraged. A lot of religious orders had trouble with keeping this balance. Also, it was not supposed to hurt anyone’s physical health, but it was easy to overdo some forms of mortification.
Second, the idea that God does not send us enough mortification through normal occurrences. St. Therese’ s Little Way suggests that life and other people are much more effective than hairshirts, and of course persecution has become much more common for religious people today.
But mortification is still accepted by the Church, and it helped a lot of saints keep their balance while living in the world, or learn self control and humility.
Catholics should not try any big change in their spiritual lives without consulting a spiritual director. Offering up small annoyances does not require permission.