When the shooting starts Jess says his magazine has 13 rounds in it. However when he engages the first shooter he only fires five shots, but after the shooter is taken out he says that he's empty, he should have eight rounds left. Plus law enforcement officers and agents almost always carry at least one extra magazine.
When Ortiz arrests the accomplice that planted the bombs one of the shooters tries to contact his accomplice on a radio. Ortiz then tries to talk to the shooter on the radio, something that an experienced agent would not do. It would have been much smarter to monitor their radio chatter to try and learn where the shooters were planning on going next.