Stupidity: Howard has the opportunity to shoot Jack at the end, but doesn't for no discernable reason; he's already committed multiple felonies, and shooting Jack would help cover his tracks all the better. In fact, he could even have just taken the cash onto the subway and left Annie behind while staying in full disguise as a cop.
Suggested correction: Howard Payne's taunting dialogue in the subway station suggests that he wants Jack to live a long life, tormented by the fact Payne was able to beat him. He doesn't become intent on murdering Jack until the dye pack goes off, ruining the money. After that, he tries to shoot Jack but runs out of bullets, then decides to beat him to death with the detonator but fails.
Stupidity: The cops in this film really aren't much help. When Jack Traven realizes that the garbage bin drop off is just a decoy (because Howard created a hole under it) and runs out to it, not one police officer bothers to follow him to the bin or down into the subway. They just decide, "Well, our job is done, Jack can handle it himself." Talk about useless.