In the wake of nearly any serious injury to a pitcher, the discussion moves to whether or not the pitcher was handled correctly, Was he asked to throw too many pitches, or too many innings, or was he allowed to throw too many of a certain type of pitch? In Fernandez’s case, you could present both sides.
His discussion was worth reading on its own, so I won't quote the rest of it here. The essential gist of it was that, on one hand, Miami handled Fernandez with care with regards to pitch counts and innings in 2013, showing caution with the young righty. On the other hand, even bringing a right-hander up that early in his career, causing such a large jump in competition (and thus stressful innings) could have led to more harm than good.
Let's address both angles. On the one hand, Miami did take care to avoid stressing Fernandez. They did this knowing that his highest innings count of his career was 134 1/3 innings the year before, and that those innings were done in Low- and High-A levels rather than the more competitive higher minor league levels. Fernandez was mowing down hitters with seemingly no problem in 2012, so his stress level the majority of the time barely registered. The team limited him to 85 pitches in his first seven starts, and he did not approach 100 pitches for some time. By the end of the season, he was routinely pitching at 100 pitches, but he never showed signs of wear and tear or significant fatigue. The Marlins then capped his innings at 172 innings, which was a decision that was made about midway through the campaign.
Up until the injury, Fernandez had been not gone through many stressful innings as well. He had averaged just under 15 pitches per inning, a mark that was higher than Henderson Alvarez in the staff but better than some of the most efficient pitchers in baseball. The amount of stressful innings he had does not seem high either. Out of 228 innings pitched between 2013 and 2014, Fernandez only had two innings in which he threw greater than 30 pitches and 39 innings in which he threw more than 20. That number of "stressful" innings represents just under 18 percent of his innings pitched.
To Cameron's second point, even promoting Fernandez up this early in his career and upping his caliber of competition may have been enough to stress his arm. But as Cameron points out in the article as well, you can also find examples of pitchers like Rick Porcello or Felix Hernandez who made similar jumps and turned out just fine. If it were the case that Fernandez was being stressed by increased competition, it certainly did not appear to be the case based on his performance and ease of innings. Fernandez cruised so well through the 2013 campaign that it is difficult to believe that this was the cause of the injury.
As Cameron finally notes, it is possible that we have no idea what could have happened. Miami attempted to do the best it could in terms of workload management for a pitcher his age and with his prior workload, and still Fernandez got hurt. It is possible that something other than workload finished off his arm. The likely culprits can be delivery biomechanics or the fact that Fernandez is simply throwing too hard. For the first, baseball still does not have a strong enough understanding of the human body and its intricate motions during pitching to make proper adjustments to mechanics. Scouts and baseball folks have some idea of what may cause future injury, but that may be due to subjective thoughts or correlation with injury rates in the past. Technologically speaking, we are still too far behind to catch all of the motions that could cause future problems.
On the second point, what could Miami really do to prevent Fernandez from 'throwing hard?" We have a suspicion (backed by recent study) that increased velocity causes more incidence of injury and possibly increases severity. There is a thought that relying on throwing a lot of sliders or curveballs could lead to injury, but this again falls back on the biomechanical impact of certain pitch types. But what could Miami do to limit Fernandez in either of these aspects? Both fastball velocity and the nastiness of his curveball are part of what made Jose Fernandez the fantastic pitcher that he was (is? We can only hope). Limiting the dominant aspects of his game is counterintuitive to Miami's desire to have him succeed. Changing his repertoire after he has worked for years using his stuff would have been silly.
Chances are Miami had no way of preventing this injury. Likewise, we have little idea whether Fernandez would have been hurt more by working September of last season or not. The Fish did the only thing they know how to do, which is to manage his workload to prevent too great a jump. It seems unlikely that that was the cause, but the world of predicting pitcher injury is still an unexplored environment for baseball. At the ground level, there is very little that we could do to predict Fernandez's special case, and the Marlins are probably not that far ahead of us either.