Many disadvantages are the opposite of the benefits. Where the barefoot runners have less impact on their joints due to going barefoot, the running shoe wearers have more impact. This is because the shoes encourage a heel strike and the running gait compensates for this. The muscles needed for the support of the feet can atrophy because they're not being used as much in barefoot running as when running shoes are on.
Running with shoes means you can run on any surface and be confident that any stones or glass will not injure and hurt you. You don't have to constantly look down to check you're not about to land on any debris. If it's very cold your feet are protected with running shoes. You're not going to tread on ice and your feet aren't going to freeze and suffer frostbite.
Because we're used to wearing shoes in our daily lives the skin on the bottom of our feet is quite tender. We're not used to running on hard surfaces connected with only our skin. Because of this at the beginning of running barefoot you may get some blisters until calluses form. The recommendation is to run barefoot sparingly at first until your feet get used to it.
Running barefoot on a treadmill
Running barefoot on a treadmill might sound like a great way to prepare yourself for running barefoot outside. However the treadmill doesn't fully prepare you for the sensation. The belt is constantly flat so, like running on shoes, you may get overuse injuries and not feel the benefit you would have running outside.
With the belt moving under your feet instead of you propelling yourself forward, your feet may get friction burns and start heating up. This is reported to have happened but isn't too bad to stop people from running on the treadmill barefoot. So it's ok to run barefoot on a treadmill if you want to. It's just not in the spirit of the true barefoot or natural running narrative.