$\begin{cases} yu_x+xu_y=u\\u(x,0) = x^3 \\ u(0,y)=y^3\end{cases}$
$\dot X(\sigma,s)=Y \quad X(\sigma,0)=\sigma \\ \dot Y(\sigma,s)=X \quad Y(0,s)=s \\ \dot U(\sigma,s)=U \quad U(\sigma,0)=\sigma^3\quad and \quad U(0,s)=s^3$
$\frac{dU}{ds}=U\implies U(\sigma,s) = Ce^s$ (1)
$\frac{dX}{ds}=Y\implies$ $\frac{d^2X}{ds^2}=\frac{dY}{ds}=X\implies \ddot X=X\implies$
$X(\sigma,s)=C_1 e^s+C_2 e^{-s}$ (2) and since $\dot X=Y\implies$
$Y(\sigma,s)=C_1 e^s-C_2 e^{-s}$ (3)
applying $X(\sigma,0)=\sigma$ has no issues to find $C_1+C_2=\sigma$, but what with $Y(0,s)=s$ or did I assume wrong initial conditions?

As I interpret your notation (since you're taking derivatives with respect to $s$), $\sigma$ is a parameter that tells you which characteristic curve you are on, and $s$ is a parameter which tells you where along that characteristic curve you are. But that's not at all how you have actually use these parameters when setting up your conditions (which don't make much sense, to be honest).
For those characteristic curves that pass through a point on the $x$-axis, say $(x,y)=(\sigma,0)$ where $u=x^3=\sigma^3$, you should have the conditions $$ X(\sigma,0)=\sigma ,\quad Y(\sigma,0)=0 ,\quad U(\sigma,0)=\sigma^3 , $$ while for characteristic curves through points on the $y$-axis, $(x,y)=(0,\sigma)$ where $u=y^3=\sigma^3$, it's $$ X(\sigma,0)=0 ,\quad Y(\sigma,0)=\sigma ,\quad U(\sigma,0)=\sigma^3 $$ instead.