Note that (to my knowledge) the missiles don't talk to each other. The RB-04 basically homes in on whatever it detects ahead of it, and you have very little control over which radar contact it chooses.
Granted, there are presets to try and encourage them to spread out, but it's always possible that they'll pick the same ship.
If they miss completely, then something has probably gone wrong. Most likely, the ship has traveled outside of the missile's search cone.
Really, the best way to make sure your missiles don't home in on the same ship is to launch, peel away, and then re-attack after the first target has been sunk.