Histogram VS Levels
The reason for this is that the lower histogram (which is used for adjusting the Levels) shows the actual raw file data before any ICC profile is applied. The upper Histogram however, shows data after the current ICC profile is applied to the image.
Normally the difference will be fairly small but, for example, you are applying B&W ICC Profile the differences will become more pronounced. The following screenshot illustrates this difference. Applying the black and white profile will cause the upper histogram to merge its RGB channels into one value where the Levels Histogram will retain the RGB values.
This feature allows you to adjust Levels more precisely while having the freedom to apply different color profiles to an image.