Those exp points contribute to the ninjas in your team to level them up, but it doesn't count towards the main's exp.

So i.e. You have your Main, Sasuke, Naruto, Sakura. When you get the exp points, Sasuke, Naruto and Sakura will all that that points that you see, but your Main will not.

Basically the same thing that food does for your current team, so kinda useless considering how many food they shove in our faces as "rewards"