Preheat oven to 375° F. Line a mini cupcake baking sheet with 10 cupcake liners or lightly grease with baking spray.
In a small bowl, combine flour, cinnamon, baking soda and salt and whisk to combine.
In the bowl of an electric mixer fitted with the paddle attachment, combine margarine and sugars and beat until light and fluffy. Add egg and vanilla and mix until combined. Add carrot and apple and mix until moistened. Add flour mixture and mix just until combined.
Distribute batter evenly to make 10 mini cupcakes and bake 15 to 18 minutes or until a toothpick inserted in the center comes out clean. Let cool 10 minutes and then remove from pan to a wire rack to cool completely.
Whisk together non-dairy cream cheese, honey and sugar until smooth. Frost the top of each cupcake with a heaping tablespoon.