This question is really about interpreting the output of the df command, which is famously confusing and if your Google for it, you'll see many questions about df.
"Size" is df results are INCLUSIVE of the 5% reserved space @chronitis told you about. This is the total ABSOLUTE space. This number will approximate the size shown in the results of fdisk -l for the partition which you're looking at in the df results.
"Used" + "Avail" provides the total EFFECTIVE space and EXCLUDES the 5% reserved space. This is the space you can actually work with.
So nothing is "missing"- the disparity between "Size" and ("Used" + "Avail") totals in df output represents the 5% reserved space
But the confusion about interpreting available space for df doesn't end there! If you delete a large file(s), but the process for it hasn't been terminated, this "free" space will not be reflected in the results of df. You'll be scratching your head thinking "But I deleted that file(s), why can't I see the additional space in df?!?" That's why when you restart, the space from the deleted file "magically" appears now in the df results.
sudo lsof +L1 will identify deleted files still showing a pid.
HTH clears up some confusion about interpreting df output. - Terrence