there are usually many reasons why your cupcakes are not flat - usually it is due to the temperature being too high for the batter (which could happen in circumstances such as modifying a cake recipe into cupcakes, or if you have uneven circulation of warm air within an oven in different shelves).
Other reasons could include overfilling the batter - I often find issues when I fill over 3/4 of each case, and sometimes they form mushroom-like tops. Good luck!
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Other reasons could include overfilling the batter - I often find issues when I fill over 3/4 of each case, and sometimes they form mushroom-like tops. Good luck!
http://www.bakingmad.com/tips/how-to-create-flat-topped-cupcakes/