In quantum mechanics it is well known that if you have a Lagrangian $\mathcal{L}$ and you want to quantise it, there is no unique way of doing this. This is because when you construct the Hamiltonian $\mathcal{H}$ and try to promote observables to operators, canonical momenta and position don't commute.
However the other way of doing quantum mechanics is in terms of path integrals. If one has a classical Lagrangian $\mathcal{L}$ then you can write down the propagator as $\int \mathcal{D}[q] e^{i S[q]}$ where $S[q] = \int \mathcal{L} dt$ is the action. It would therefore seem like $\mathcal{L}$ uniquely specifies the appropriate quantum theory, at least for any measurement that only involves propagators.
So my question is: how can one have non-uniqueness for canonical quantisation but apparent uniqueness for path integrals if the two formulations are supposed to be equivalent? Is it that the propagators do not fully determine the theory? Does this then mean that there are some quantities that cannot, even in principle, be calculated with path integrals?