Computers represent numbers (and other things) imperfectly, sometimes for convenience, sometimes because there is no alternative. Complement arithmetic is easier to implement than sign-magnitude, but has a few quirks.
We just live with them, there's nothing special here.
In two's complement, the "extra one" is also there, but it is added during the change of sign, and because there is only one representation for zero, the system is a bit more elegant.
Try to picture a base complemented number as representing what's missing in the number to reach $b^k$ ($b$ is the base, $k$ is the number of significant digits). The apparent "extra one" is due to the fact that what is counted here are the steps to reach the implicit "zero" in $b^k$.
For instance, in ten's complement, with $k=3$:
$-5 = 995=10^3\color{red}{-5}$
In nine's complement, $999$ is zero, so the extra one is not necessary in this case. It becomes necessary, though, when the operation causes overflow due to change of sign:
$-5 = 994$
$-5+6 = 994+006 =\color{red}{1}000\color{blue}{+1} = 001$