PURPLE HULK deficiency's or just a strain look? See below to notice the abnormal look of first few leaves growth. The smaller two are different strain

Starting life is difficult. It's not unusual for the first few sets of real leaves to show some signs of their hard life but that usually works itself out pretty quickly. For the most part I think your plants look good and you are off to a good start. I think auto's should be started right in their final pot. They have a very limited lifespan and you don't want to waste any of that precious time recovering from transplant shock. I also find it easy to over water or let little cups dry out. I'd get them into their big girl pots soon and always make sure the Ph of your water is good.