Line a 9×13-inch baking dish with parchment paper, including up the sides. Spray with nonstick cooking spray.
To a large sealable plastic bag, add pretzels. Using your hands or a rolling pin, roughly crush them into smaller pieces.
To a medium bowl, add about ⅔ of the crushed pretzels, reserving the rest for the topping. Add the cereal to the bowl of crushed pretzels, mixing to combine. Set aside.
To a large saucepan over medium heat, add the sugar and corn syrup, stirring to combine. Cook until boiling.
Stir in the peanut butter until smooth.
Remove from heat. Pour the corn syrup mixture over the pretzel cereal mixture. Gently fold to coat.
Using an oiled spatula, press the cereal mixture into the lined baking dish.
Meanwhile, to a microwave-safe bowl, add the milk chocolate and butterscotch chips. Heat the chips in 20-second intervals, mixing in between, until they have melted and the mixture is smooth with no lumps.
Pour the melted chocolate and butterscotch chips over the bars, smoothing with an offset spatula.
Scatter the reserved crushed pretzels over the top.
Let the bars sit for about 10 minutes before cutting and serving.