Well, you must be doing something (or several somethings) wrong.
First thing, Read The (Friendly) Manual for the paint. No, really, study the label on the can, and if there's additional info on the Web go print it out. Don't just blow it off.
Build a paint booth like control for the application area - take a fan and a furnace filter to get a clean air source, then hang plastic to keep any falling dust away.
The gun has to be really clean - If you can't get the gun clean enough, go get a new gun. Sometimes they have vortices in the airflow that encourage the paint to clump into drops that create goobers in the end finish. Or it isn't shutting off completely.
When they tell you to strain the paint going into the gun, that means they know it has a history of creating clumps in the can, and that strainer is insurance.
Use a proper stroke, don't be afraid of wasting a little paint. You should NOT be pulling the trigger with the nozzle aimed at the workpiece, you squeeze aimed off into space at one end, then sweep across the surface being painted, and don't release your finger till you are in clean air on the other side. Goobers are formed and tossed when you're pulling the trigger and starting up the paint flow through the gun.