Either A. he's changing color, B. he's growing his winter coat and usually a horse's winter coat is a different shade than the summer coat, or C. he's going to end up a chocolate palomino.
A. He could be changing color entirely. A lot of foals are born a different color than what they will grow up to be. For example, gray horses are never, ever born gray. They are typically born bay or chestnut, and over the next few years will turn gray with each change of season.
B. He could just be getting his thicker, winter coat. Many horses will have a lighter coat in the summer, and in the winter they will get much darker. For example, my horse is a very light blonde bay in the summer, with stripes on his withers that litterally look yellowish. However, in the winter time, he is almost black.
C. He could be turning into a chocolate palomino. Here are some picture examples. I'd have to say it's one of my favorite coat colors, and the "spots" you are seeing could be dapples.

