Furthermore, it is entirely normal ... it is entirely okay ... for even a fairly large amount of the storage space to be "fragmented." Fragmentation is not necessarily a bad thing at all. You don't want to pull a fragmentation-percentage number and, at some magic number or another, say, "OMG! It's fragmented! Fire! Fire!"
Fragmentation was a big deal when the filesystem-de-jour was FAT (which was originally engineered for floppy disks) and a 20-meg disk drive was "big." But that was a long time ago, in a galaxy far away.