The Riots Myphos card says to put 3 Stamina tokens per player on it, also place 1 Stamina token per player as a Ongoing Effect. at the end of every Myphos Phase. Do these Stamina tokens come from the Stamina bank or the actual lnvestigators.

I don't have the card to check right now, but I'd say from the reserve. Some investigators would die automatically otherwise, since their max stamina value is 3.

l wondered if some low Stamina lnvestigators were meant to die as they are caught up in a riot.

Fingolfin is right, the token you add are taken from the reserve. You pay from your actual stamina in order to remove token from the Mythos card