Each game is made up of many, many little things that can change the outcome of a game.
I did comment that it seems to me that umpires tend to often call a ball four on a 3-0 count a strike if it is reasonable close to (but not in) the strike zone just as I think they tend to call a pitch on the edge of the strike zone on a 0-2 count, a ball. In this game, Arrieta had the count 0-2 and made a tremendous pitch that was right on the edge and clearly in the strike zone, but the call was a ball, and yes, it made a huge difference in that inning and in the game.
Things like this even out over a long season and good teams usually, though not always, overcome and find a way to win. In baseball, even the very best teams lose quite a few games.