How does aunt Polly’s behavior poke fun at some of the medical practices of her time

I think that you are referring to chapter 12. Aunt Polly, concerned with Tom's health, practices a multitude of home-remedies and cure-alls on Tom. Gullible when it comes to quack periodicals and medicine, Polly tries everything from water-treatments to feeding him "Pain-killer."

The "Pain-killer" became a regular treatment, and to Tom, it tasted like liquid fire. Tired of the daily doses, one day Tom feeds a spoonful to the cat, which upon receiving the medicine begins to do somersaults in the air while "spreading chaos and destruction in his path." When Polly learns that Tom has fed the cat the painkiller, Tom explains for his actions by saying that he "done it out of pity for [the cat] ­ because he hadn't any aunt" to "burn him out" and "roast his bowels."