I think I'm missing something important here.
For a fluid with a velocity $u$ in a pipe with cross section area $S$, the volumetric flow rate is equal to:
$$Q_v = uS$$
If we now consider vectors, the volumetric flow rate is:
$$ Qv = \int \vec{u} ·\vec{n} dS$$
Where $\vec{n}$ is the normal vector to the cross sectional area. For example putting numbers, considering only one axis $x$:
$$ \vec{u} = 10 \vec{i} \qquad \vec{n} = \vec{i} \qquad S = 10 \\ Qv = 100$$
However from the divergence theorem we know that:
$$ \int \vec{u} · \vec{n} dS = \int \nabla · \vec{u} dV$$
And for incompressible fluids $\nabla · \vec{u} = 0$, so it would give $Q_v = 0$.
Obviously i'm doing something very wrong here, but I cannot see what. Am I considering something wrong in these equations? Is the normal vector in the divergence theorem refering to another surface in this case, or to both surfaces, these being, both $\vec{n} = \vec{i}$ and $\vec{n} = -\vec{i}$?