There are a lot of dilemmas that Bean faces. One dilemma is that he is so much smaller than everybody else. The other cadets immediately treat Bean as completely inferior to all of them based only on his looks.
Another dilemma is that Bean is smarter than all of the other cadets . . . including Ender. As you read further into the Bean series, you will learn that Bean isn't even likely 100% human. He's been created and engineered and changed to the point where he just isn't the same as a human. Bean doesn't know all of this in "Ender's Shadow," but he knows that he is quite different. He knows that he is smarter than his classmates, Ender, Graff, everybody. It's hard for him to know this, but not know why.
It's also a dilemma for Bean to know what needs to be done, but never have anybody believe him or want to follow him. It takes him most of the novel to earn even a modicum of respect from his fellow cadets.
As the novel progresses, it becomes clear to Bean that Ender is falling apart. Ender isn't capable of handling the onslaught of "training." He's making dumb mistakes and working himself past exhaustion. Bean knows this long before anybody else notices it. Bean knows it, but even Ender himself thinks everything is fine. The dilemma for Bean is how to help Ender continue to lead without Ender noticing Bean's help.