If they are breaking through your main defenses, think about that is happening: a big wave comes in, your turrets are flooded, and a bunch of stuff sticks in your tractor beams. Your turrets shred all that, but it might take a few seconds or even a minute. Meanwhile, the raid starship is immune to tractors and so slips through. It would take a long time to kill, so unless you manually gave your turrets a raid starship priority, they probably will focus on the smaller ships first so that the tractor beams can be freed up to stop more ships.
Meanwhile that raid starship slips past almost unscathed with nothig even shooting at it anymore. It makes a beeline foe your command station on that planet, probably, and goes right through the forcefield and quickly kills it.
There are three problems here:
1. There is too much congestionin your main defensive area for the raid starship to be shot much.
2. There is a long stretch where the raid starship is crossing the distance to your command station and meeting not resistance.
3. When it gets to your command station, even if you put turrtmwta there, it kills your command station so fast that your turrets don't have time to do their job.
Normally it's the job of tractors to "hold while you punch," so to speak. And if that fails, then the force fields can do the same. For any ships where that doesn't work, you instead need to use very different tactics. Turrets have a long range, so are great for making "corridors of pain" through which ships have to fly to get to your command station. Mines can also work for this, just not with raid starships. A dreadnought or two stationed in that corridor could also work wonders. Gravity turrets could also be used to slow that ship, though it slows your ships, too. A zenith space-time manipulator (or several) could give your ships a needed boost in speed to catch fast ships like this. Higher mark command stations have a lot more health and could give your nearby turrets more time to fire at the raid starship while it's whittling away at all that extra health. Paralyzers, if you have them, could be great in the corridor of pain. Decoy drones, if you have those, could be used to draw the fire from your command station while your turrets do their work.
There are definitely a lot of ways to go.
hope that helps!