 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. 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. They had spent so much time in prisons that it was sometimes hard even for them to remember what they really were, outside. The inside guard finished putting the new prisoners away and turned off the tangler field once more.
 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.