Similarities:
They both had a childlike mind and an innocence in the world. Neither had any idea of how horrible the Holocaust was nor did they realize how much it was affecting them. Their death together in the gas chamber showed their curiosity and their sudden fear, but they had no idea that they were going to die. Their bond together was despite their cultural differences and a literal fence.
Differences
Their main differences were that Shmuel was a Jewish child in a concentration camp and Bruno was the son of a Nazi commandant. Bruno had questions and was curious about why Shmuel was wearing "pajamas" and why he had a number and a shaved head. Bruno had no idea what was going on in the camp. Shmuel, on the other hand, had no idea what the life was like on the other side of the fence.