Simply put, it's the way Windows handle it.
To better explain it, right click on your drive and select Format.
Just click on Close to choose not to format it.
You will see a section called Allocation Unit Size.
Each sector has 4096 bytes (the default).
When files occupy it, they take up a certain amount of space.
For example, the first file has 2000 bytes. It will use up the
first 2000 bytes. That allocation unit now has 2096 bytes
left.
Say you have a second file, 3000 bytes. It can no longer use this
particular allocation unit, as there are not enough space for it.
It will now use the second allocation unit.
Each and every file are saved this way. If there's enough, it will
use the same allocation unit. Not enough, it will use the other.
The previous allocation unit won't be used even if there are enough
space for it.
This caused the amount of hard disk space used to differ from the
actual size of all the files added together.