The passage you reference is talking about connections within the motor cortex in the brain. Afferent/efferent can be confusing terminology in the brain.
In the periphery, the terms have clear meanings as you say: efferents go to muscles, afferents carry sensory information back to the CNS. No real controversy there. However, the meaning of "efferent" is just outwards/away from; afferent is the opposite, meaning towards. In the context of the periphery, we consistently use these terms in relation to the CNS: efferents go outwards relative to the CNS, afferents go towards. If the terms are used in the spinal cord, the convention is to relate to the brain: afferents are signals heading towards the brain, efferents are heading towards the spinal cord (and then likely to the muscles next).
Within cortex, you're already in the brain, so it makes little sense to talk about afferents or efferents relative to the brain: we are already in the brain so neither makes sense unless you are talking about cells that specifically project outside the brain. Instead, we use the terms with respect to whatever structure we are in. Confusingly, that means nearly every axon in the brain is simultaneously both an afferent and an efferent, it's all a matter of perspective. If you are studying thalamus, you could refer to efferents projecting to cortex; your friend studying neocortex could refer to afferents projecting from thalamus. They could be the very same axons.
In the Rahman et al 2013 paper that your link is referring to, they are talking from the perspective of cells in motor cortex, and when they refer to afferents they mean axons projecting to a cell in motor cortex. Really, they almost could have dropped the word "afferent" and just said "axon" throughout the whole paper; probably the only reason they used the term is because they are not talking about descending axons leaving motor cortex headed towards the brainstem/spinal cord, they are talking about axons terminating on cells in cortex.
Rahman, A., Reato, D., Arlotti, M., Gasca, F., Datta, A., Parra, L. C., & Bikson, M. (2013). Cellular effects of acute direct current stimulation: somatic and synaptic terminal effects. The Journal of physiology, 591(10), 2563-2578.