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.
If you put cupcakes in before the oven is ready, it will mess up their baking process. Also, ovens can be finicky. Invest in a good oven thermometer, and then use it! Double-check the temperature of your oven before you put your cupcakes in.