I always figured that each prisoner's name, including Ulfric's, was added to the list after the prisoner was captured. It isn't a most-wanted list. For whatever reason, no one added your name to the list when you were captured. Maybe you didn't tell them your name. Maybe the Imperials handling you did not know that they were supposed to get your name. Maybe they were too busy with other things at the time and simply forgot.
For Tullius to have pulled off his ambush, he must have had a spy at the highest levels of Ulfric's command. Someone with access to Ulfric himself, because he knew exactly where Ulfric was going to be, and how many soldiers he would have with him (yes Brynwulf Free-Winter, I am looking at you). My assumption is that Brynwulf also gave Tullius a list of every Stormcloak soldier whose identity he could learn. Tullius would want that after the war is over with, so the he could lop all their heads off.