One of the, let's say, oddities of the new replay review system in Major League Baseball is that the so-called "neighborhood play" at second base on a potential double-play ball is not reviewable. That is, if a shortstop or second baseman is trying to avoid contact from a runner and bails from the bag before he receives the ball on the relay, it's still going to be counted as an out.
So the difference here is that shortstop Jordy Mercer wasn't off the bag to avoid contact but was instead forced off the bag in order to catch an errant throw. Thus, the ability to challenge and overturn the call.
Obviously this is going to be a learning process, but this is an important distinction to note moving forward with the new review system.