How are you putting them together? Are you letting the cupcake portion set up before you pipe on frosting or is it still damp?
Not knowing your process makes it difficult to speculate, but if I had to hazard a guess, the cupcake portion is drying at a faster rate and/or shrinks at a greater ratio than the frosting you're piping on. You may wish to try letting the bottoms dry a bit or completely first? Just an idea from a scientific standpoint (sorry, I don't actually do cupcakes, but someone here is bound to know more!)
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