Sure. Just like a breeder could produce a pup out of the right size standard with shelties. Or a dog with an under/overbite. The breed people are not going to demand that this line be outcasted and have people recommend them to stop breeding because they have these throwbacks. There wouldn't be any lines if this was the case, as each line has produced some fault at one time or another. It is the breeders responsibility to identify where that fault came from and breed out that fault.
It is a different story when the line has something that is fatal or seriously hinders the dogs life....such as eplipsy, certain cancers, hip displasia, etc.
It is just that in agility there are some big names out there....that are always producing the top dogs in the country. So when a dog from that line has a problem the name is known

I don't have a ton of experience with this in regards to shelties, but I am very familiar with this in setters.