Let us consider, for example (all though the question applies more generally) the 1D wave equation $$ u_{tt} = c^2 u_{xx}.$$ This has characteristics $x-ct = const$ and $x+ct=const$ which is readily observable by factoring the differential operator as $$\frac{\partial^2}{\partial t^2} - c^2\frac{\partial^2}{\partial x^2} = (\frac{\partial}{\partial t} - c\frac{\partial}{\partial x})(\frac{\partial}{\partial t} + c\frac{\partial}{\partial x}).$$ Thus, making the variable transformation $\eta = x-ct$ and $\xi=x+ct$ yields $$ u_{\eta \xi} = 0 $$ from which we conclude that $$ u =F(x-ct) + G(x+ct) \tag{1}\label{1}$$ for some sufficiently smooth functions $F$, $G$.
If we consider the IVP: $u(x,0) = f(x)$ and $u_t(x,0) = g(x)$ we derive d'Alambert's solution from (1). However, this is the solution for a boundaryless domain and is incapable of capturing any sort of boundary values. e.g. a clamped boundary $u(0,t)=u(L,t)=0$. Yet, this is a well posed problem and solvable via separation of variables. So we can only conclude that (1) is not the general solution. What went wrong?
My guess is that in making the variable transformation and integrating we implicitly assume a certain global regularity which the boundary value problem does not satisfy. Any clarification or expansion on this?
To get the analogue of (1) in a more general case, e.g for an inhomogeneous boundary problem, you can put $$v = \left(\frac{\partial}{\partial t} + c\frac{\partial}{\partial x}\right)u$$ so that $v$ solves the transport equation $$\left(\frac{\partial}{\partial t} - c\frac{\partial}{\partial x}\right)v = 0.$$ You can solve that equation explicitly with the caracteristic method. Then, you can solve in the same way $$\left(\frac{\partial}{\partial t} + c\frac{\partial}{\partial x}\right)u = v$$ to find $u$ in terms of $v$.