No, this is not common. But some files are ignored such as temporary internet files. So if you were surfing while Defraggler worked that could be the explanation. Try to run CCleaner or another program that can delete cache & cookies and then run Analyze in Defraggler. Did that make any difference?
An easy way for cleaning is:
1. Start -> Run -> write -> shell:cache -> highlight all files -> right click an file delete. Say no if promt asks if you want to delete non-temp files.
2. Start -> Run -> write -> shell:cookies -> highlight all cookies -> right click an choose delete. Say no if promt asks if you want to delete non-cookie files
Even CCleaner is not that fast!