Who finds the two boys when Bruno crosses the fence?
The specific answer to your question is "ten soldiers" who remain unnamed. Here is the exact quotation:
Right at that moment, there was a loud whistle and ten soldiers--more than Bruno had ever seen gathered in one place before--surrounded an area of the camp, the area in which Bruno and Shmuel were standing.
Bruno has crossed the fence for two reasons: to have a last "goodbye" with his friend before going back to Berlin and to help Shmuel find his father. Shmuel even has a set of "striped pajamas" that "don't smell very nice" ready for Bruno. Right before the previous quotation, Bruno and Shmuel are talking about the sadness in not being able to find Shmuel's father. Their conversation is cut short by the "ten soldiers" and the "loud whistle." These soldiers are whistling in order to get the people to "go on marches." What the boys do not realize is that the prisoners will be marched directly into the gas chambers and killed. Therefore it is unfortunate that the "ten soldiers" find the boys while they are together on the same side of the fence.
In Chapter 19, Bruno decides to help Shmuel find his father by crawling underneath the fence and dressing up as a Jewish prisoner to avoid detection. Once Bruno enters the concentration camp, he mentions to Shmuel that he doesn't like the camp and feels uncomfortable. When Bruno tells Shmuel that he wants to go home, Shmuel reminds Bruno that he promised to help him find his father. Unfortunately, the boys cannot find any evidence that would lead them to Shmuel's father and Bruno decides to walk back to the fence. As soon as the boys turn to leave, however, ten soldiers surround the area of the camp where they are standing and command everyone to begin marching. The boys are never specifically discovered by any soldier or prisoner, but they are forced to march with a group to the gas chambers, where they eventually die.