The color of a kernel of corn is determined by its outer pericarp layer. For this discussion, we use New York Red Flint as our example.
Aptly named, New York Red Flint has kernels that are predominately red; however, variations in the genetic expression of a kernel's pericarp layer creates the variable appearance in the depth of the red color. Some cobs will have kernels that are a deep red while the kernels on other cobs might not be so red. For some kernels the red is so pale, that the endosperm layer dominates and the kernels appear yellow. This genetic variation is normal and expected.
Of course when we select kernels for our seed stock we are selecting for a deep red which explains why the Cob Tips & Butts offering of New York Red will have kernels that are yellow and is intended for culinary use and not recommended for planting.