He did well in the first half. Nothing wrong with his judgment. I don't think every referee would have awarded a penalty for a friendly push like the one Ajax player Van der Wiel gave. But Clattenburg was in his right to do so.
In the second half Ajax players realized they had to score so they started attacking (without result). Then the extra time came and the 30 minutes of hard work all or nothing football proved too much for the English referee. He did not see elbows being put in faces, he did not see Huntelaar being held by the Croat goalkeeper, he had difficulty keeping up with the pace. It was all too much for Mark Clattenburg.
And Clattenburg's assistants were completely wrong a couple of times. It's not often that you get to see such bad assistant referees. When a referee is busy running around trying to keep up, his assistants should be the ones to see what happens in the box, to notice players hitting each other. They didn't. And sure, it's difficult to judge off-side when players are quick and standing on the edge, but more than twice the distance between the last player and the forward was large enough to park a truck in. Awful.
Ajax, once upon a time a great club, seemed to have sold most of their good players and replaced them with nobodies. For some reason the coach, Ten Cate, thought it a good idea to defend the 0-1 result from two weeks ago instead of scoring some more goals. And this was a home match. The same Ten Cate who told the press a few hours later he was going to Chelsea as an assistant to the new coach there. Maybe he came to the conclusion he is simply not good enough to be the main man.
Dinamo Zagreb, by the way, did well, played it very smart.