Thicker gelatin layer at the bottom of the dish
If you pour jello into dishes while it is still very warm, the mixture has time to start layering and separating a bit, leaving the layer you describe on the bottom of the dish. In my experience, the best way to avoid it is to not pour the mixture into the dish/es until it is cooled to nearly room temperature and considerably thicker. While it's cooling, you can stir it periodically to prevent layering, and then it should set quickly enough that it won't separate.