This question is really about interpreting the output of the df command, which is famously confusing and if you Google it, you'll see many questions about df.
How to interpret df's output
Size in df's 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 reviewing 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's output represents the 5% reserved space.
Free space not accounted for in df's output
If you're scratching your head thinking "But I deleted that file(s), why can't I see the additional space in df?!?", here's why:
If you delete a large file(s) but the process for it hasn't been terminated, this "free" space won't be reflected in the results of df.
sudo lsof +L1 will identify deleted files still showing a PID.