As a rule, a CTE will NEVER improve performance. A CTE is essentially a disposable view. There are no additional statistics stored, no indexes, etc. It functions as a shorthand for a subquery. In my opinion they can be EASILY overused (I see a lot of overuse in code in my job).
Check the cupcakes at the minimum baking time. If the recommended baking time is 18-22 minutes, check them at 17 or 18 minutes (just a quick peek, make sure not to let too much heat out of the oven). If the tops are rounded and no long appear wet, they may be done.
The tips at Cupcakes Take the Cake concur: If recipes don't specify mini baking times, note that minis will take more than half of the baking time recommended for standard size cupcakes. My survey of a number of mini-cupcake recipes shows the general consensus is about 10 minutes, or half the time of a regular cupcake.