What is your oven temp and how long are you baking them. To me they might be cooking too fast.
What is the recipe and the amount of ingredients?
Some cake recipes are formulated to be this way. Depending on where you got it, there might be an explanation that it will rise in the oven and then settle back down once it cools. For a cake a flat top is exquisite. This could be true for cupcakes too unless you want a flat top. This is why I believe that cake recipes are not the same for cake recipes.
The other reasons could be too much liquid, oven not the right temp, opening the door, etc.
But post your recipe so that we can see the ingredients.
BTW if they taste good, just stick the frosting on top and no will be the wiser. I made a batch of cupcakes that looked just like this. I watched as the bubbles in the batter came to the surface and popped. I tweaked a recipe and put too much liquid that created too much steam that caused the bubble show I saw. It was disheartening, but they were the best cupcakes ever. My DD took them to work and people were coming back for seconds. Sometimes a bad cake is the best tasting cake. And frosting hides a lot of sins.
Having looked at them again I'm going to say the recipe is formulated to flatten out when cooled.
What is the leavening in the recipe?