Oven temperature, your baking soda/baking powder or mixing can all cause a misshaped muffin. Temperature - It's important to make sure your oven is accurate with an oven thermometer. 350F is the optimal temperature for perfectly rounded muffins. Expired Baking Powder/Soda - You should change your baking soda and powder at least every 3-6 months after opening it. It can still work after that but it won't work as well and eventually stops working altogether. Over Mixing - with muffins you want to mix your batter as little as possible once the flour is involved. that is why with this recipe, I have you mix the wet ingredients thoroughly before adding in the dry. The dry is mixed into the wet enough when you no longer see flour. If you're worried about it, you can let your batter sit for 10 minutes before baking.