The main cause is the New Technology File System, or NTFS.
When you first install Windows, or format a new NTFS partition, a few things are created. The two that matter here are:
- The Master File Table, or MFT, which is usually contiguous, reserved space for storing file metadata, like location, size, acls, and timestamps.
- The unreserved space, where data is placed.
What makes it worse is the partition does not have to fill up to much cause this. If you delete a file and create a new same size or smaller file, Windows may not place the new file in the space of the old file. The data may be placed instead sparsely [source]. This further increases the distance between the data and the MFT. Other file systems do this as well because it avoids fragmentation by giving files room to grow, which is exactly why Microsoft implemented it in NTFS5. These other systems do not try to store their metadata in one contiguous space though. Ext2, for instance, stores its metadata in inodes, which reside in block groups, which are placed throughout the partition [source].