It is very common for the atmosphere to have wind blowing in multiple directions between the different layers, called shear. Usually the jet stream will be around 90 degrees offset from the layers above or below it. If you open up https://www.tropicaltidbits.com/analysis/models/?model=gfs and click or select any region to get into the model sounding viewer, there will be wind direction barbs off to the right of the map that show the shear vertically.