The first one is concerned with identifying someone who was definitely at the crime scene. The second one is simply asking who else may have been there, perhaps to gather witnesses.

The words "else" and "it" make it impossible to fully interpret the sentence without additional context. "Else" eliminates some specific people. The sentence itself does not indicate who that might be. There are numerous possibilities. "Else" might eliminate someone who is known to have been at the crime scene. "Else" might eliminate someone who is known NOT to have been at the crime scene. (For example, "We know it wasn't Jack. Who else might it have been?") There are many other possibilities. "It" points to someone specific but unknown person who was at the crime scene. "It" might point to the person who committed a crime. "It" might point to someone whose fingerprints were found there, or to someone who was seen leaving the building. The possibilities are endless to whom "it" might point. However, the sentence cannot be spoken unless the specific nature of what "it" points to is first made clear.

In the first one, someone unknown was definitely at the crime scene. In the second one, some might have been there, they might not.