While I was shooting my 07 Scion TC I began getting large craters
near the roof and windows. I was told that it was because of a silicone
based product such as armorall. Does anyone know the best way to remove
and prevent it from happening again?

wash the car with dawn soap.

I've never seen fish eyes that bad..

Always wash the car first, with warm soapy water when it comes in for repairs (as lild said, some of the degreasing dish detergents can be best). Its also a good idea to wipe it with wax and grease remover before starting any repairs. IF you are concerend about fish eyes, change your wipes frequently and wipe it a couple times. Then do your repairs, prep etc. Once it is ready to paint, clean it with water based cleaners (personally, I have found the aersol glass cleaner to be the best general purpose) then clean with a final wash solvent (or wax and grease remover). Again, being sure yo use fresh lint free paper towels and change them frequently.

This works most of the time. You can buy fish eye eliminaotr for most paints (to go into the clear or SS top coat). This can stop or reduce the amount of problems you have, but should only be used as a last resort.

This can also happen if your detail station is too close to your paint booth or prep station. All the waxes, tire shines, and cleaning products that are sprayed can get sucked into the spray booth. I've also seen this happen if a diesel engine is running near the booth or the air intake of the booth(not as bad as the picture). A clean paint job is a happy paint job.

Well, the basics are.... wash the car before you start sanding! furthermore wash it before u start working on it. That alone will save u a lot of headaches.

the best way ive found is wash the car and come back with thinner in the wheel wells and all the cracks that u think might hold some silicone or anything that could cause the paint to fisheye and if its a car with a lot of silicone all over it ill wash the panels down with a strong degreaser and then come back with thinner a few times

Products like Armorall and WD 40 are difinately are a painters nightmare. Personally, I do not allow either product in my shop. There are many effective degreasers on the market but an old painter once turned me on to an inexpensive product that I have found to do better than any. It is purchased locally in "Dollar" or "Dollar General" stores and is found in the cleaning product section. It is called "Awesome" and can be purchased for around $1.00 for a 16 oz spray bottle. Refills are also available. Might want to give it a try and wipe all areas adjacent to rubbers and trim where dressings may have been used. I also use it to clean all jams prior to paint.

Wow that's really bad.

Looking on the bright side, at least you can definitely see it's caused by surface contamination through improper cleaning, rather than being an airborne problem. There's little point me going through what has already been described perfectly well above, but suffice it to say - clean, clean, and clean again