Re: combat that don\'t make sense
 

Seekers don't target fighters at least not if you play unmoded game. They are capital ship missiles and can't target small and agile targets as fighters.

Some mods may have such seekers probably as a version of point-defense system.

Re: combat that don\'t make sense
 

Seekers work just fine targetting fighters.
Seekers work just fine targetting other missiles, too. (Needs v1.94+ in simultaneous mode)

Never EVER make them point defense, however. In such a case, every single PD missile in your fleet will be launched at the first fighter/seeker to move. Really bad tactics.

Instead, let your ships all fire on random targets manually. Instead of 150 missiles pasting a single stack of 5 fighters, you can have a beautiful wall of seekers popping fighters throughout the enemy fleet in a massive bombardment.

Note: this also presumes that you do something to fix PDCs, so that missiles are worth using, yet at the same time not overly powerful.
Turning off the auto-fire is one of the best things you can do.