I cant really tell the dimension through the picture but the fist thing that comes to mind is insect larva. are they raised bumps or just discoloration
Looks like you got some pH problems buddy. Purple stems and rust spots say phos def and calcium def. Im more than confident is that ur pH is off and needs to be corrected. Good luck budy! =)
spider mites. Get some neem oil or azamax n treat the shit outta those fuckers by hand thouroughly 2-3x over the next week, then by and release some lady bugs, they'll finish and maintain the sich