Paint and Body.

First of all, lets get one thing out the way. Rust!!

Rust has over the years been a vehicle owners worst bugbear. It has got better over time with manufacturers using better quality materials in building their vehicles and most of them pride themselves on having a perforation guarantee that will cover a good ten years.
You can replace a mechanical or electrical component, but bodywork is a different kettle of fish. It's not as simple as just changing something over. Sometimes, welding and painting could be involved and that can take anything from  a few days to a few weeks to sort.
But rust as a problem in itself will stem from two points.

A: From behind the panel out.
B: From the panel surface.

If your vehicle is presenting a rust problem, first of all it will need investigating by your local dealership / garage bodyshop. They could possibly determine the cause in a few minutes of looking at the vehicle.
If its from behind the panel, there's a strong chance it will be covered under warranty, but that may need investigating further.
Further investigation will also determine whether the vehicle is presented in the same way it left the factory, unmolested and without modification.

If however, it is surface rust, there isn't anything a manufacturer will do to cover it by warranty. A vehicles bodywork is prone to the elements and as much as vehicles are tested to their extreme before launch, extreme testing is only carried out under official legislations. And if a vehicle stands up to those tests under legislation, thats as good as it will be when it comes to market.

Most surface rust points are presented by disgruntled customers pointing to their now unsightly bonnets. All we can say on that one is, keep your concrete foot off the accelerator pedal. As a vehicles paint is tested to legislation. Anything over that legislation is often tested by the customer, normally in the form of a heavy right foot.

Debris flicking up off the road will hit a vehicle all the time and your vehicle will bounce them off like water off a ducks back. But only at certain speeds. If you're driving your vehicle like you've stolen it and lets face it, given the opportunity, you will, then debris hits your vehicle at increased velocity. This then opens up the possibilty of chipped or damaged paintwork. It has nothing to do with paint quality. Don't fall into the trap of taking on board what is said on the forums.

Out of all customers that present these "Spots", it is normally a vehicle that has a bit of "Oomph". We never saw little old grannies coming in with the same problems with their cars that couldn't pull the skin off a rice pudding, so its clear what happens.

Don't be surprised if you are turned down for warranty work if you present your dealership / garage with this issue. It will most likely become a personal repair, paid for by yourself.

COVERAGE
In terms of coverage on bodywork, most manufacturers warranties will be very similar indeed. But it is always worth checking with your local establishment first.
The majority of manufacturers will only cover body imperfections on the waist down (Under glass). That means, all pillars and the roof are not covered by a bodywork or paint warranty.

The reason behind this is because panel work used for these areas aren't susceptible to water ingress, that can sit and cause rust from the inside. So if you have a rust spot that appears there, it will definitely be a stone chip of some kind.

PAINT RUNS
If you notice a run in the paintwork, depending on how old the vehicle is, will determine whether it will be a warranty issue or not. A run just doesn't appear in the paintwork.
If its a new vehicle and after a while, you notice there is one there, theres a good chance that it will have been there at the time of its assembly.
If its been missed at all the various quality checks, then you need to have a chat with the dealership / garage Service / Aftersales Manager, who will undertake the necessary process to get it sorted for you. Different establishments will have their own process in order to deal with such an issue.

If its a used vehicle, theres a good chance that it may have had a smart repair. Don't fret about this, it is quite common. Trust us, as a customer, half of you part exchange a vehicle in that requires a good deal of prep work, including body and paint.
Dealerships can't sell them in the condition they were given to them in, so a degree of work is agreed before being able to be retailed again, fresh for a new start with a new owner.
However, these won't be covered under a manufacturers warranty, but may almost certainly be the responsibility of the repairer that carried out the paintwork.

-Will B ;)