How do I get rid of and prevent small rust hole?

IF there is one spot of rust coming through it sounds like there is some rebar close to the shell surface. We used to have to chip out the metal and patch the spot. If it is just an imperfection in the marcite or other coating, a small amount of undiluted acid can etch it away slowly over a few applications.

I agree with Road Lizard on the cause. If the hole is very big, I personally would want to patch it so it will not re-occur. You can use a small epoxy patch, if it keeps reoccuring after acid treatment. They sell epoxy sticks at most places such as pool supplies, building supplies. I attached a link just so you know what I'm talking about. If you get it at a pool supply, you may be able to find white. The one in the picture is gray. Epoxy Putty :: Oatey.com (http://www.oatey.com/Plumber/Shared/ProductGroupDetail/93/Epoxy+Putty.html) If the link doesn't work just go to Oatey web-site, or rectorseal also makes one.

It is 2 part epoxy. You pinch off a piece of the "tootsie roll", you knead the a/b together until consistent color. Then you apply to a clean, wire brushed surface. It will dry under water in 20-30 minutes. You will have to keep pressure on it until it sticks pretty well. Use gloves. It will take days to get it off your hands!

This is similar to the magic putty that they have been advertising on TV. But, it has been around for years. I've used it many times for lots of different things. Including repairs just like you are making.
Al

Is this an above ground pool or a inground concrete pool?I think you may be talking about a metal above ground pool, right?