You obvously don't think it normal that our thoughts alone could cause wounds to appear on our bodies. So there must be some supernatural cause.
God provides what is necessary for a people. It could be that such stigmata were not a part of His plan before the turn of the millennium.
Also, as was pointed out, the use of a corpus on the cross developed prior to the stigmata. If intense meditation on the wounds is required, it may be that before the use of crucifixes, there was no such impetus to such contemplation.
SD