Spotlight may not have completely indexed the drive, or it may have been interrupted at some point. To force Spotlight to reindex, open your Spotlight preferences and go to the Privacy tab. Drag the Macintosh HD volume into the privacy section, then remove it from the Privacy list using the - sign. You'll know you have done it correctly if you see a dot pulsing in the Spotlight menu in the upper right. Let it sit for a few hours and when it stops pulsing it will have finished indexing the drive. Then run a search and see if it can find other files in your home folder.