100% logical fragmentation on 99% empty disk

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Hi, I have a 2012 R2 server with SQL server 2012, and the disk layout is like this:

D - Data

L - Transaction Log

T - temp DB

S - System DBs

and I got an error via scom about 100% logical fragmentation on Drive L and T.
this is a virtual server and the storage managed by NetApp,
and when I checked the drives and their content I saw that drive L contains only 100mb of Data out of a 10GB drive, and T was the same...
when I checked the SQL I didn't saw any internal fragmentation but in the optimize drives I saw 100% fragmentation...
and when I did defrag with the task in the task scheduler it did nothing and the fragmentation level remained 100%...
can someone explain to me what does this fragmentation means and how it is on 100% if the drive is 99 empty?

I've asked in SQL Server forum but they told me its related to this forum...


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