Fair enough, i can see your reasoning. However, you look at the incident predominantly from a defenders point of view.
Every footballer has a right to challenge for a ball, but whether they can without contravening the laws of the game is the issue.
The defender was,caught out of position because his team was caught out of position. The defender has the legal challenge right to block the shot, but that's not what he did.
Due to his bad positioning and accurate play from City (which by the way is what goals are mostly built upon) he lunged into the attacker, missed the ball took out the player and that constitutes a penalty kick.
I would even go so far as to say it was an out of control challenge that endangered the opposing player.
Apart from the dangerous challenge the exact same scenario happens for the 2nd penalty, and everyone agrees that's a stonewall.
That's how I see it.