Do i need to prune these? am I watering improperly is there too much moisture in the bottom of the dish or pot? Do i need to raise the smart pot off the dish so that oxygen can get to the roots that come out? do I just leave them and this is nothing bad?
Getting to the root of your questions: Do not prune the roots as that would be very detrimental to the health of your plants (it would not kill them, but it would slow down the growth of your plant), its impossible to tell if your watering improperly as i dont know the amount of water you are using and how often you water, I would take the smartpots off the dish because it is collecting excess drain off from when you are watering that the plants roots and bottom layer of your growing medium are just sitting in, which isnt ideal for the roots.