Take note of Zapruder's testimony in this dialogue below... Zapruder follows the line of thought that Kennedy was hit on the right side of his head, and that the shot came from behind him... and that he was in the line of fire...
This fellow shooting from the pergola window is likely what Zapruder heard...
Mr. ZAPRUDER. Yes--after the shots--yes, some of them were motorcycle cops--I guess they left their motorcycles running and they were running right behind me, of course, in the line of the shooting. I guess they thought it came from right behind me.
Mr. LIEBELER. Did you have any impression as to the direction from which these shots came?
Mr. ZAPRUDER. No, I also thought it came from back of me. Of course, you can't tell when something is in line it could come from anywhere, but being I was here and he was hit on this line and he was hit right in the head--I saw it right around here, so it looked like it came from here and it could come from there.
Mr. LIEBELER. All right, as you stood here on the abutment and looked down into Elm Street, you saw the President hit on the right side of the head and you thought perhaps the shots had come from behind you?
Mr. ZAPRUDER. Well, yes.