I can see two scenarios:
1. Built-in Windows defrag isn't as intense as 3rd party ones.
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The Windows defrag isn't that bad actually, having defragged with windows, check with some other defrag tools and you won't find any fragments. I also have Power Defragmenter, DeFraggler and JKDefrag.
These confirm the windows defrag does what it says on the tin, whilst the last two have many more bells and whistles and options selective defragmenting, moving files to optimise their loading, leaving some space at the start of a partition, etc. etc. All of these are fine, but over an above a simple defrag which windows defrag does fine.