TOM
If we catch these guys do you think we'll be able to find out who's backing them?

MICHAEL
That's not the catch -- unless I'm very wrong, they're dead already. They're killed by somebody close to us -- inside. Very, very scared they botched it.

TOM
What about your people ROCCO and NERI? You don't think that they had something to do with this.

MICHAEL
You see -- all our people are business men, their loyalty is based on that. Now, one thing that I learned from Pop was to try to think as people around you think. Now on that basis, anything's possible.

CUT TO: Outside, DEANNA screams
DEANNA
Right out my window! I want to get out of here! They're lying there dead!

CUT TO: BUTTONMEN running to the drain.

BUTTONMAN
Over here there's two of them. Looks like they were hired out of New York, I don't recognize them. We won't get anything out of them now.

MICHAEL
Fish 'em out.

[Two BUTTONMEN fish out the bodies]
TOM
Alright, get rid of the bodies.

ROCCO
Where's Mike?

TOM
ROCCO.

[TOM walks off.]
CUT TO: MICHAEL walks into ANTHONY's room.

The answers are right there in the script. Michael states that it is a inside job someone close who got scared when the job was botched. Michael shows that he thinks just like his old man and the suspects are mainly Rocco or Neri.
Deanna gives the final clue with her line
"Right out my window! I want to get out of here! They're lying there dead!".

Now there is no refrence to how they died but they are dead. Fredo may be weak & dumb but I am sure he rose to the ocasion to cover his ass and kill them both.

The phone call to Fredo from Johnny Ola in a later scene confirms Fredo as the inside man.
That is the "No Luke I am Your Father" twist to the movie.