Despite being an extremely robust process, it has two disadvantages. One, it is a two-sided process. It needs access from both sides to form a weld. This is not possible in a production environment where there might be limited access to the other side. Second, is the issue of chipping. Chipping is the formation of small hair-like whiskers that protrude from the weld pool. In an ideal process, it is desired to have all the chips enclosed underneath the head of the fastener. But, these small hair-like structures extrude away from the weld pool. This causes accelerated crevice corrosion and diminishes the aesthetic appeal of the joint.
You can learn more about chipping in friction element welding here.