Over mixing can add too much air to your batter. When you put cupcakes in the hot oven with too much air in the batter, the hot air will only make it seem as if your cupcakes are rising as the air escapes, causing the dreaded deflation.

Should cupcakes be flat or domed?

The air is the problem. You would have to put so little batter in to avoid the air reaching the middle to cook with no dome but then you ruin the cupcake with an uneven baking and an overdone bottom.

Why did my cupcakes not rise?

Over-beating the batter:

Over-beating your batter overworks the gluten, making it tough and less likely to rise. Another analogy is that you are beating in too much air which will then escape once your cupcakes are out of the oven, causing them to shrink.