As stated fisheyes are caused by contamination on the surface. They can also show up when you try to paint when it's too cold and apply too wet. It can also be contamination from the compressor in the form of oil, diesel fumes near the compressor, old air hoses which might have been hooked to an automatic oiler at the compressor, oil from other tools in the air fittings, or water in the line.
I assume you have the parts in bare metal and you are trying to put on primer or sealer? I will bet since they are parts in the engine compartment you didn't clean them enough prior to getting them in bare metal. If you have grease and/or wax on paint or a coating of any kind and you don't clean thoroughly prior to sanding you sand those oils and wax into the metal.
The best way to fix it is to use Dawn soap and wash, rinse well and dry to prevent flash rust. Then saturate the surface with a rag of thinner. Use another rag and wipe it till it's 100% dry. I suggest you do that at least twice. I would then use a wax and grease remover (also known as degreaser) from your local autobody distributor. After you tack it off put on a VERY light dust coat of primer or sealer. When I say light you should back the gun off the surface and use a light trigger. I f done right you should be able to see droplets on the surface and see thru it. Let that flash and put on another slightly wetter coat, let flash and then put on a few much wetter coats. If you do that you will be fine but if the compressor and lines are the cause of the fisheyes then you must fix that and do the above steps.