First of all, both cupcakes and muffins are delicious. Now that that's out of the way, let's get down to business. The saying, "Cupcakes are muffins that believed in miracles" has successfully achieved creating a deeper meaning while also having a humorous undertone attached to it. Who wouldn't want to listen to encouraging words while staring at a delicious cupcake?
In a nutshell, what this t-shirt is trying to say is that anything is possible. Turning a muffin into a cupcake obviously isn't something that happens on a regular basis, if at all, but having faith is key. You can do and be whatever you want to be as long as you believe it. Whether you're being told by a human, or by delicious desserts, the truth will always be within your belief in yourself.