 In the end, what was it that O'Leary smelled throughout the story?
His name was Liam O'Leary and there was something stinking in his nostrils. And, what was more important, why she couldn't adjust herself to it, now that she was in. And O'Leary was a man who lived by the book. That old witch Mathias never told me I was supposed to mop up. Captain O'Leary took a long drink of water from the fountain marked "Civil Service." If anything, she had had a better environment than O'Leary himself, and look what she had made of it. A bleary old inmate orderly stood up straight and touched his cap as O'Leary passed by. When you're in it, you don't much care what it is called; it is a place for punishment. She was in a detachment of three unfortunates like herself, convoyed by an irritable guard, climbing the steel steps toward Block O from the floor below, when she heard the yelling. The two guards turned to see what was coming in as the three new candidates for the Greensleeves slumped to a stop at the head of the stairs. Now O'Leary knows I hate it when there's a woman in here. The outside guard pulled the switch that turned on the tanglefoot electronic fields that swamped the floor of the block corridor and of each individual cell. While the fields were on, you could ignore the prisoners—they simply could not move fast enough, against the electronic drag of the field, to do any harm. It was like walking through molasses.
 The riot. He picked up on the growing unrest, and it came to him as a smell.
 Burning flesh, from Bradley sitting on the bench and hurting herself.  The riot. He picked up on the growing unrest, and it came to him as a smell.  The blue pills the Warden was taking, that were warping his perception and ultimately kept him from realizing the riot was brewing.  Burning flesh, from the shive being formed. It's the "trouble" he was detecting.