This is still very early in Batman's career. Sure, he's had all these years of training, but he hasn't had a LOT of experience out on the street with these lunatics yet. This was shown well in "Batman: The Man Who Laughs", which is the official first appearance of The Joker in Gotham City. Bruce was trained to fight off the murderers, muggers, rapists, corrupt city officials, etc., but never in his wildest dreams, did he think he would face something like The Joker. The Joker is also VERY clever and sneaky. He's also moves very quickly. All it takes is a still-slightly-green Batman to get distracted for just a second, and The Joker is out of Batman's grasp....and running off, laughing, into the night.....or knocking him out with a crowbar or a sucker punch or something.
BTW...great community you guys have here. Looking forward to being a part of it as the movie's release draws closer.