Not really Shotacon, seeing as the male Zeroes are both the same age...
Nisei towards Seimei. In a biiiig way.
Yayoi has a brief moment of this upon meeting Ritsuka for the first time:
Yayoi: Aoyagi Ritsuka. He's pretty. Like a girl.
Also, in regards to the Les Yay Koya and Yamato, adversaries in the third and fourth volumes of the manga. Note that this was actually made more explicit in the anime, which in their first scene showed them kiss on the train when the manga just had them hold hands, as if it was just to make sure we weren't mistaken as to what was going on.