The stations have a part that isn't suppose to be there

Which stations?

I only know of the mining station, research, and the citadels from the ship appearances

Fixed the stations, what do you mean by "citadels from the ship appearances"? Are there unintended pieces showing up in ship entities?

I meant when I went into ship appearances and I go to the citadel it would show the part but it was just the citadel not the ships

If you're using the carrier patch bit, I'm about to pull it on account of it causing other problems. I updated the shipset here to "just work" with the odd battleship-entity based carrier set NSC updated to, so they (the "Carrier patch" and this shipset) aren't going to be truly compatible at this point. Turn off that mod, and it should go back to normal.

I turned off the carrier patch and the part is still there

Which ship/which race?

it was for all four races

Which ship though?

sorry i might've messed what i said but i'm talking about how when i go to ship appearances and i look through the different ships. When i reach the citadel it shows the mammalian citadel head with the exe online citadels you created. sorry if i was unclear

There isn't a "citadel" in the shipset, that must be from another mod? The ship classes this mod applies to are corvette, destroyer, cruiser, strike cruiser, battlecruiser, escort carrier, battleship, dreadnought, carrier, flagship, titan, and juggernaut.

I didn't mean the shipset. I'm talking about the star base citadel sorry if i confused you

I'm not able to view starbases of any quality in the ship appearance section of the nation builder or the ship designer, so I'm not sure how I can help you. This mod isn't compatible with whatever mod is allowing you to view those outside the actual game.

If by chance you're referring to the "Headquarters" from NSC, this shipset mod does not do anything to replace it, and so the default HQ model shows.