It is often said that QG is a topological QFT: given a bordism between $D$-manifolds $\Sigma_1$ and $\Sigma_2$, QG assigns a unitary between the Hilbert spaces associated with $\Sigma_1$ and $\Sigma_2$. For simplicity, here we won't sum over topologies, even though this is widely believed to be the right thing to do in general.
Concretely, the Hilbert space $\mathcal{H}_\Sigma$ associated to a $D$-manifold $\Sigma$ is the space of complex functionals $\Psi:Riem(\Sigma)/Diff(\Sigma)\to \mathbb{C}$. Note that these states are diff-invariant by construction, and so no spatial-diff constraint must be imposed.
Now, it's my understanding that in a TQFT, the Hamiltonian $H$ must vanish identically. To see this, fix the background topology $\mathbb{R}\times\Sigma$, with $t\in\mathbb{R}$ interpreted as time. Then all the bordisms are the identity bordism, so the evolution from $t_1\times \Sigma$ to $t_2 \times \Sigma$ is just the identity. But the generator of time translations is $H$, so we must have $H=0$.
On the other hand, in canonical quantum gravity, the Hamiltonian constraint of classical GR is quantised and leads to the Wheeler-de Witt equation $H|\Psi\rangle=0$. This equation is supposed to be a nontrivial constraint, selecting a "physical" sector of $H_\Sigma$. Much effort has gone into constructing explicit solutions for $|\Psi\rangle$. It surely can't be the case that $H$ vanishes identically on $\mathcal{H}_\Sigma$, otherwise no one would talk about "solving" the WdW equation.
What have I misunderstood? In answering, please feel free to assume $\Sigma$ is closed, compact and without boundary, if this simplifies things.