I think that the understanding of non-verbal cues is only a minuscule piece of the puzzle of alienation that leads to nerdy ways and escapist tendencies.
The inability to understand such cues (alongside other symptoms which are nonetheless similarly associated with stereotypical nerds) is often given a name - Asperger's Syndrome, or more generally, half the spectrum of autism. After all, normally our understanding of other's physical cues is either built-in or rapidly learned at an early age, and only a select number of problems can interfere with that, one of them being an inability to learn these things naturally. I'd suspect that these disorders are far more common in minor forms than their diagnosis is, because it is a very subtle difference that people often decide to call weirdness or oddity.
However, despite the commonality of autism-like disorders, it would be quite mad to decide that this particular problem with cues is the sole cause of the "Nerd factor", or social rejection. What about low initial social status from wealth and ethnic disadvantage, the grief of losing family members at a fragile age, extremely challenging personal or family problems, depression and other mental diseases, and parental neglect? All of these can make a child unable or unwilling to interact with others in a fluid way, leading to more issues and eventually to escapism. There is never just one issue which if solved will improve everything, which is why it's not an easy thing to defuse on a mass scale. Therefore, I must disagree with the title of the article and that of the study, both of which suggest that the "study reveals why 'nerds' get bullied", because the study is clearly not exhaustive enough to reveal all causes.
Similarly, it makes no sense to say that only 10% of students experience bullying in their lifetime. The experience is, by all accounts I've ever read, universal to kids who go to school. That figure is just too low to be believable. I can see that a numerically similar statistic is in the linked article, but it is given with a different meaning, that 10-13% experience rejection. A much more specific experience, but even so, who is kidding themselves that there is anyone who has never experienced the rejection of their peers, let alone that this demographic is the majority of all school-age kids? No child who knows other children, no matter how popular they are, could escape that, plain and simple.
Science is a very good tool for asking questions, but more often than not the results are exaggerated and their meaning is perverted by interpretations of a very subjective nature. Scientists, being under pressure to produce definitive, exhaustive and useful results, may even exaggerate these factors about their own research if there is funding demand involved, leading to drastically altered conclusions. This particular research seems to stand as an example of precisely that occurring, or else it is the product of some other logical interference. Plainly, it does not stand up to the highest standard of logic, though some of it may be useful in understanding children's problems if we were to underrate the exhaustiveness of the research relative to the article's conclusions.