Neither scoring nor goal difference is the main problem, really. Those stats usually reflect the heart of the matter, but not always.
What matters in football is to control the key moments in the game. That's where a match is being decided, and that's where the best players eventually pay off in both ends. It's small margins; 30-40 seconds or so out of the full 90 minutes in most cases. More often than not, Courtois will save that one on one if it comes down to it while Szczesny will concede and/or get his ass sent off because he's not as good. Henry will score the goal that turns the game in our favour while Giroud will miss.
Chelsea had the players last season who came out top nearly every time in those key moments. We didn't.