He was very close to the play (sometimes even stood almost in the line of the pass) and he decided to be generous on both sides. Generally, this worked well with both disciplined teams and the three cautions were by the rulebook. He varied his whistle tone when needed and only gave free-kicks when he couldn't opt for an advantage. He was well balanced considering both sides and was well respected by the players.
Towards the end, the limits of the generous approach were obvious. I wouldn't say that Rizzoli wasn't aware of this but for a real 9 he needed to react to this. He didn't and so Badstubers challenge (80') plus verbal provocation passed unpunished as did Muller second challenge on the goalkeeper (88'). If he had sent off Muller for this, it would have been harsh for his card policy but possible. I think, the knee to the face in the Swiss box was borderline, but not really a justified penalty appeal.