This may be a bit too extreme and complicted but this is possible:

I think that there may have been a bunch of hitmen (not just 2) that shot through Michael's window. There may have on only 3 hit men in total (who knows). In preparation for after the assassination attempt, Roth or one of the superiors could have told one hitman to kill the other two hitmen right after they killed Michael, thus cutting off any traces. Roth could have been like "Hey, Tony after you guys kill the Don, make sure you take care of Jimmy and Johnny in front of Fredo Corleone's house."

The fact that their throats were cut (from Contractor's comments) indicates that they were murdered close-up and meaning they were probably killed by someone close to them.

This is all I can figure.