The only possibility is that there was another member of the group of "shooters" who killed two of them and then somehow managed to get off of the compound. The other possibility is that Fredo did it.
When Michael is talking to Tom about this whole thing he implies that he has a theory about the whole thing because he says something like If what I think happened happened, then I have to leave tonight. Then he says that that he thinks that the shooters are dead already, and, "they're killed by someone close to us...inside....very very scared they botched it."
The very next scene is Deanna screaming that there are dead guys right outside her window. This suggests it could be Fredo, who in the conversation with Tom, Michael describes as "weak and stupid."
Another clue comes much later in Havana. By then Michael has confirmed the traitor was Fredo because Fredo made the slip about knowing Johnny Ola. Of course Mike set him up for that by asking him point blank if he knew Johnny, and Fredo lied and said he didnt.
In other words, I think Michael suspected Fredo from the beginning, but he had to be sure. What clinches this theiry is what Michael says to Fredo in the famous kiss of death scene. "I KNEW IT WAS YOU FREDO...."
Also,