Its actually a pretty common issue lately. Sometimes the shingles just don’t match perfectly out of the bundles. It has nothing to do with the instillation method. More than likely it will be more and less visible at different times, depending on how the light it hitting it. Sometimes, it does get less noticeable as the roof “weathers” but not always.
Also, has the roof had a good rain yet? Once in a while we end up getting shingles that have a powdery substance on them which makes them look a bit off until the first good rain.