ATried my first completely scratch carrot cupcake recipe today. While they taste EXCELLENT, they turned out a little puny :( It called for all purpose flour but I subbed cake flour. The recipe calls for 1 1/2 cups all purpose flour and I subbed 1 1/2 cups & 3 Tbs of cake flour. I have a feeling this had something to do with the sinking. I'm thinking my measurements for the substitution was off... Anyone had this issue before?

I don't know if it had anything to do with the sinking or not, but why would you substitute flour, especially the first time making it? 

I am not into all the science of baking and all, but I wonder if the softer texture you are trying for isn't compatible with the weight of the carrots and other add ins for carrot cake.

I had the same problem with a yellow butter cake. I made 2 square layers and 12 cupcakes. My layers turned out beautifully. My cupcakes looked wonderful when I took them out of the oven but sank in the middle when they cooled. My layers didnt sink and it was all from the same batter. This is the second time it has happened to me. I don't know.

A

I'm thinking that may be the issue too.