My 3D model is missing 2 pins and I have no idea would could be the reason for this.
RV1 does not have a 3D model.
It looks like you have disabled the solder mask layer for the two pads on the right.
The other 4 pads also do not look proper. Maybe there are rings on the silkscreen layer?
I propbably should have clarified that the upper 3 pads form 1 part and the bottom 3 pins form another part. They are parts i had to draw up myself. Both literally consist of only pins. The visible pads are fine. but the missing ones are giving me an headache, since all layers are enabled.
I don’t see footprints on the PCB.
Did you create symbols and footprints and place those in personal libraries then add them to your Schematic and PCB?
Welcome to the forum 
One small point, is there a reason why the upper 3 pads that form 1 part have a smaller diameter than bottom 3 pads ? I confess that I don’t yet fully understand the problem are they 2 devices like 2 TrimPots please ?
As always: which KiCad version? And there is little evidence for diagnosis. It’s best to post the project here. From the file menu you might want to create an archive and post it here.
Posting the project may help, but you could start with a better description.
I also do not see pins on a 3D model, I don’t even see a 3D model, so I don’t know how to respond to that.
Your RV1 is also confusing. Apparently it’s two different footprints, but that brings more confusion about what is actually missing.
You show a screenshot, but you do not write what is wrong. Are you having problems with the two pads covered with green? What about those other pads with the white rings? White does not look right for THT pads (With standard KiCad color scheme).
Btw, I changed the category. IMO this is more about footprints than about 3D models.
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