Did the text really spell the word "twelve?" I would have expected it to be written and punctuated this way:
I was tapping my teeth with the pen, pondering 12 Down.
By the way, it's interesting that the speaker mentions a pen. Yes, serious crossword puzzle solvers make a point of using a pen. They are deliberately making it harder, because it prevents erasing and correcting. (I always use a pencil myself).