This is a natural occurrence in non-homogenized milk. When you shake the bottle the cream will loosen and break up into the milk. The best way to shake the milk is with a rocking, side-to-side motion. This allows the milk to get around the cream and break it up. If you've been shaking it up and down, you are not doing anything wrong but it may take a little longer to mix back in.
Other ideas are to spoon it out for your coffee, eat it with fruit , or enjoy on your cereal as a special treat.
To prevent the cream top from plugging the top of the bottle, some customers store our milk by laying it horizontally in their refrigerators. This also makes the cream layer thinner making it easier to mix.