This could be Bradbury's way of foreshadowing Montag's interest in books and his opposition to the firemen and the Mechanical Hound. But we can speculate that the Hound was reacting to how it was originally programmed. In other words, the Hound was reacting to the scent or sense of the chemicals which make up the physical material of a book, or of some other suspicious object or person.
Maybe the Hound is so advanced that it can sense pheromones or Montag's anxiety and the Hound is able to calculate that this anxiety stems from a conscious or subconscious interest in books and freedom of thinking. In other words, perhaps Montag's brief encounter with Clarisse had already begun to change the chemical reactions in Montag's mind and the Hound is even sensitive to this.
The most plausible explanation probably does come from his encounter with Clarisse. She touches him with the dandelion. There are three possibilities. The Hound is picking up on Clarisse's DNA which had rubbed off on Montag. She is already regarded by the authorities as a suspicious free thinker. O, the Hound is picking up on some scent of a book which was passed from Clarisse's hand to Montag's chin. Or, the Hound is picking up on the scent of the dandelion itself. Since most people spend their time glued to the parlour shows and ear implants, maybe no one experiences or even touches nature. The Hound might be set to be suspicious of anyone with traces of nature.