Does a character that incaps a mystic with two tokens take damage cause of the one penetrating damage they take.

I think they would. Incapacitate is an attack that deals no damage but it is dealing penetrating damage to a 2 tokened character. Mystics activates with damage from an attack.

That is correct. If Incapacitate is used to apply one penetrating damage to a Mystics TA figure that already has 2 action tokens the Incapper will take Mystics damage.

Let's quote the game effects in question and work this out

Yes, Incapacitate will trigger Mystics if it deals the 1 penetrating.

Ok thanks guys