Bear in mind that the missiles resolve as salvos, not individual missiles, so that if the missiles are fired in salvos of 10 missiles, they will all retarget on a single new target, and if one takes the new target out the rest are lost. Its not a really effective action to fire large salvos at light targets such as fighters or GB (you'll get a lot of overkill) - I usually find that salvos of 3 or 4 missiles work best there.
Another problem with fast moving units like Ftr & GB is that the followup salvos dont start searching until they reach the last known position of the initial target, so if you have a long stream of follow ups the remaining (potential) targets can move out of the sensor range before the missiles start looking - more than once I've seen squadrons of fighter & missiles pass through each other and then the missiles stop & stay put behind the fighters boring in on my delicate battlefleet.