Here are some helpful solutions for the common causes:
To ensure a pebbly surface, avoid overmixing the muffins. Use 15 to 20 light hand strokes. There should be some lumps in the batter.
Outdated leavening can cause sunken tops. Most brands of leavening carry expiration dates. Be sure to check the date at the grocery store as well as each time you bake. After purchasing new leavening, date the container. Then, use within 6 months of opening. Also, keep baking powder cans tightly covered. If baking powder absorbs moisture from the air, it will be ineffective as a leavening agent. Learn more about leaveners.