Barefoot running has gained popularity, and there is no report in the available scientific literature suggesting frequent injuries. In contrast, there have been a flurry of reports regarding minimalist shoes which raise concerns about their safety.
A report by Hollander and others found that a variety of minimalist shoe did not duplicate the mechanics of barefoot running. This was predicted on this website years ago. The reason is that footwear by definition much have a sole as an interface between the plantar surface of the foot and supporting substrate that remains attached to the foot. This attenuates mechanical transients required by plantar surface SA II mechanoreceptors which are used by humans to maintain both localized loading of foot structures and aggregate vertical loading (peak group reaction force) at safe levels. Hollander and others, as most biomechanists fair to comment on neurophysiological control mechanisms due to the compartmentalization of scientific disciplines.
Hollander, K., Argubi-Wollensen, A., Reer, R., Zech, A.Comparison of minimalist footwear strategies for simulating barefoot running: a randomized crossover study. PLos One; 10(5) 2015.
A report of relatively high quality measured bone marrow edema via MRI as recreational runners changed from traditional running shoes to Vibram FiveFingers shoes. There was a substantial rise in bone edema particularly of forefoot structures with the FiveFingers shoes, which indicates some damage and repair of these structures. Users of minimalist shoes seem particularly prone to metatarsal fractures which are uncommon with normal running shoes. This is explained in this website by both lack of plantar sensory feedback and lack of posterior calcaneus protection with minimalist shoes.
Ridge, ST., et al., Foot bone marrow edema after a 10-wk transition to minimalist running shoes. Med. Sci. Sports Exerc. 45:1363-8; 2013