This doesn't always happen and is normally only clearly visible on black and dark colored vinyl rolls. It tends to be more prevalent on rolls that are tightly wound thus creating more pressure between the vinyl and the paper backing.
The vinyl is in no way ruined or unusable. It is simply a cosmetic problem. You can take a piece of mottled or blotchy sign vinyl and lay it in direct sun and in about 5 minutes it will be perfectly glossy. You can also take a hair dryer and carefully remove the "blotches" with heat.
Mottling is a special consideration for vinyl films. Mottle looks like a haze, or blotchy dull spots on the vinyl film surface. This condition occurs when the glossy top surface of soft, conformable vinyl film is pressed against the release liner in a wound roll.
While conformability is a benefit of vinyl films, it also makes them prone to mottling. Factors affecting the level and severity of mottle include heat, time wound in a roll, roll tightness, film formulation, and liner type. Also, film color and gloss level have an effect. Mottle will show up more on higher gloss films and darker colors.
Mottle can be reversed. To eliminate mottle, unroll the vinyl and leave it lying in a warm area. Or, carefully use a heat gun (or hand-held hair dryer) over the film surface. The mottle should begin to disappear. Once film is applied to a substrate, most mottle will eventually disappear with time and exposure to heat or sunlight.
You may also notice "lines" in your vinyl. This is caused from the vinyl being rolled onto the cardboard core, which has imperfections on them. This can also be fixed by letting the vinyl "relax" for a bit and using warmth from the sun to help it return to its original state.