For a most thorough understanding of the phenomena of the stigmata, consult the “Mystical Doctor” Saint John of the Cross, in The Living Flame of Love, and The Spiritual Canticle.
";;;if God sometimes permits [a spiritual] effect to extend to the bodily senses in the fashion in which it existed interiorly, the wound and sore appear outwardly, as happened when the serpah wounded St. Francis. When his soul was wounded with love by the five wounds, their effect extended to the body, and these wounds were impressed on the body, which was wounded just as his soul was wounded with love.
“God does not usually bestow a favor on the body without bestowing it first and principally on the soul. Thus the greater the delight and strength of love the wound produces in the soul, so much greater is that wound produced outside on the body, and when there is an increase in one there is an increase in the other. This so happens because these souls are purified and established in God, and what is a cause of pain and toment to their corruptible flesh is sweet and delectable to their strong and healthy spirit…” (Living Flame of Love, 2:13)
One of St. John’s main points about the stigmata is that they represent a rare physical climax to the interior spiritual experiences previously granted by God to the soul in contemplative prayer. The interior spiritual experiences which he terms “wounds of love” are a normal - however uncommon - part of the life of prayer!