In the Middle Ages, when the method of writing texts and manuscripts changed and the use of feather-pens was intoduced, the letters of both the
Latin and the
Greek alphabet changed. Non-capitalized letters were introduced for the first time and later different forms of both the capital and non-capitalized letters started to emerge. Today we might call these hands.
In Medieval Greek the prevailing form of writing in manuscripts and texts became a type of a semi-cursive writing, in which letters merged with one another to create a new form out of the two old ones (ligurates). An example in the Latin alphabet is the evolution of the sign '&' from the Latin word 'et' "and"
One of these new signs in Greek was a combination of the letters sigma (in its final form) and tau. This new sign was named after its two "parent" letters: stigma.
Gradually the sign stigma became the most common of all these signs and people began to use the word 'stigma' as a generic term for any kind of sign. In this way the plural of the word stigma - 'stigmata', which originally meant only 'signs', became almost unintentionally the most prevalent name for the wounds of Jesus when he was laid down from the cross.
The word 'stigma' itself (in the singular) began over time to have a negative connotation and 'signs' began to mean 'prejudices'.
This is the explanation of the stigma of the word 'stigma'.