Before we go any further, here are some important concepts/disciplines that need to be kept in the forefront of your paint work.
Adhesion: (as applied to painting) The ability of spray on chemicals to stick to a given surface.
In this case primers, filler, paint, etc...... In order for paint to stay on reliably, each sub layer has to stick/adhere to the one below it. There are two types of adhesion, mechanical and chemical.
Mechanical adhesion is provided by the sanding scratches you apply to the surface when sanding/blocking the surface. These very small scratches create random cuts in the surface with rough groves, the primer/paint will flow into these and when dry form a mechanical bond. It's important to sand between coats of primer to maintain the mechanical adhesion.
Chemical adhesion is accomplished when two layers can be chemically bonded together. For instance: base coat color, can have a chemical bond with clear if the clear is sprayed within 24 hours of base coat application. Times vary by product brand but the information is usually available on the paint can or on the product application sheets available (usually free) at the paint store.
Substrate: Applied layers of products up to the application of paint is the substrate.
There is a reverence and discipline that need to be kept with respect to substrate. Your substrate starts the minute bare glass is exposed, keep it clean.
From this point on oil, gas, grease, spray lubricants, silicone lubricants, hand lotions and any foreign chemical substance is your enemy. Even oil from your hands can cause substrate issues. How you ask? Fillers & primers are porous and will absorb them, it's very hard to remove them completely. In some cases, I've had to remove the problem area of all substrates and start all over. I've seen wd40 mist/fumes float across the room and ruin the following paint application. I can't stress this enough, friends who come over to check out your work always seem to want to see with their hands. They just can't help it, they have to feel how smooth the primer is........ This is NOT OK.... I keep a used sanding block available to slap some sanding dust in my hands to absorb the oils before touching the substrate. Once you start sanding the dust sticks to your hands and keeps oils dried up. If your friends want to touch, slap their hands with it too. I've startled more than a few by yelling "DON'T TOUCH THAT" in an aggressive tone.
It's very risky to combine mechanical and paint work. An engine change while the car is in primer is very risky. Kid with a chocolate bar, oh no, No, NO!......... Don't even think of lubing the door, hood or top hinges with any kind of spray. There seem to be an endless source of these contaminates, keep the discipline. Lacquer thinner can work to clean bare glass but often will remove primers.
These foreign substances impact adhesion, paint will not stick to oils and other substances, if you spray primer over it, it will absorb up into that layer too. The paint may even go on ok, but the hot/cold cycle of shrink/expand will soon separate the layers causing a bubble under the paint. Silicone is the worst as it causes the paint to repel away from it like the same end of two magnets. This leaves a paint void, usually a small circle (fisheye) in the paint. These are not often visible in the primer, usually showing the first time when paint is applied. They make fisheye removers but the ones I've tried don't work very well. It's much better to keep the discipline of substrate cleanliness. Washing bare glass with dish soap and water then letting it dry completely before the first coat of primer is a must.
Keeping the substrate pristine isn't as easy as it sounds. Try to limit the time of exposure by moving forward with the work at every opportunity. If it's got to sit for awhile put a car cover on it and don't store anything on top of it.