A lot of this is down to the players you have. You don't have a quality striker, and Mourinho has sacrificed quality in midfield for energy and work rate. Eden Hazard is pretty much your only midfielder who ever looks like scoring. So the team as a whole are severely lacking in goals. Bayern on the other hand have a similar problem with there lone striker as you guys do, Mandzukic and Pizarro aren't prolific 25 goals a season guys, but there midfield more than makes up for it, with the likes of Ribery, Robben, Gotze, Muller, Kroos and even Shweinsteiger pops up with a few
I don't think Cahil helped matters either, strolling off the pitch wound them up, and then he should never have come back on again wasn't up to it