From what we do know about crystal formation, there are four possible reasons for this problem. The first and most common is idiopathic. This means it happens for no apparent reason. There may be a reason, we just don't know what it is.
Secondly, it could be hereditary. Some families just seem to have this problem. The exact genetic link is also still unknown. Metabolic diseases, especially affecting the thyroid, is a third cause of crystal formation. The joints are affected most often but the discs may be affected, too. And finally, trauma or surgery (a form of trauma) can start the process of crystal formation.
Crystals have been found in herniated discs. Adults 60 years old and older are affected the most, so it's likely age-related. How much crystal deposition contributes to disc degeneration and herniation remains unknown. It does apear that crystals forming in the disc accelerates or speeds up the degenerative process.