For me, it was a 100% clear penalty. Willian went for the tackle and came in completely late much after Walcott had moved the ball away with his touch. There is clear contact between Willian's foot and Walcott's and the ball is no where near. That is the definition of a foul.
For me, a foul is a foul regardless of where on the field it happens. A penalty doesn't warrant a 'stronger than regular' foul for it to be called a penalty. Willian's challenge would for sure have been reprimanded if it were outside of the box.
Also, the refree didn't give some clear-cut cards. Azipiluteca (sp) had a really atrong tackle on Arteta/Ramsey (can't recall) in the beginning of the match. Should have been a clear yellow. Mikel's challenge is one where 8 matches out of 10, you get a straight red for. I understand if one says 'They were both going for the ball with cleets up, Arteta got there first, etc...' Ok, whatever. But not even giving a yellow is a freakin' joke. And 5 seconds later not giving the penalty makes me say WTF. In a tight defensive display like this, even a yellow early on makes a huge difference and can distrupt the defender's gameplan. Imagine Mikel and Azip not able to commit so much defensively, it could mean the collapse of Mourinho's gameplan.
It was clearly Mourinho's game plan to affect the game's mood and tempo with hard fouls. The refree promoting this by overlooking all the fouls was terrible management. As expected, the temper of the game rose afterwards, and Arsenal players as well began to go in for hard tackles, etc (no surprise about the Ozil-Ivanovic hustle). Of course these were all benefiting Mourinho and his 'grind-it-out' gameplan.
Usually, I don't pinpoint the ref. However, in a game like this, where one team is trying to grind it out second by second and play so negatively, even the tiniest detail makes a difference. Even one yellow not given can tip the scales in a game like this. Not to mention the penalty in a game where if you score one, you're basically guaranteed to win.
Also, it is normal for Chelsea to have more chances. They were defending 11 men and Arsenal naturally had to put everything up front. They were bound to give chances at the back, while Chelsea were likely not to give any. You can even consider it a shortcoming of Chelsea that they couldn't score against a team so willingly exposed at the back, while still giving Arsenal some clear chances. Remember, even that fantastic Barca team couldn't pass this cynical tactic in the CL a few years back. Considering how defensive Chelsea were, I think it should be commended that Arsenal still had some really important chances. Mainly, Giroud's two chances which were clear-cut. IMO, he had to put those away.