the combat visualizer makes it look like a lot of missiles impact against targets which have already been destroyed. if this is the case, it's probably one of the reasons missiles suck so bad when compared to hitscan cannons- missiles aren't being used efficiently, with ships missing the opportunity to attack valid targets in favor of targets that are doomed anyway.

if not already present there should be some kind of check to make all wings and defense structures look for a new target if their current (non-missile-protected) enemy target is about to be destroyed by other missiles that are en route but have not impacted yet.

missile units should probably always preferentially switch to unprotected targets if both protected and unprotected targets are in range.

to reiterate http://ministry.kronosaur.com/record.hexm?id=1841, the visualizer also makes it seem like missile equipped units don't start firing at maximum range, which should also be looked into.