Thicker gelatin layer at the bottom of the dish

When I make Jell-O (fruit-flavored gelatin or jelly), I often get a patchy skin of "thicker" gelatin on the bottom of the dish. The color is the same, but the "skin" has less flavor and a much harder texture.

My assumption is that some of the gelatin granules aren't getting completely dissolved; however, I can't see any granules remaining (or I'd keep stirring it). Am I right about the cause? How do I prevent or reduce the problem if there isn't any visual cue?