Let $\phi$ denote the Klein-Gordon field. Then its propagator $\langle 0 \mid [\phi(x), \phi(y)] \mid 0 \rangle$ can be calculated as $$\int \frac{d^4}{(2\pi)^3} \frac{-e^{-ip(x-y)}}{p^2 -m ^2}. \tag{1}$$ Isolating just the $p^0$ part of this integral, which is where the problem is, we get $$\int \frac{dp^0}{2\pi i} \frac{-e^{-p^0(x^0-y^0)}}{(p^0 + E_p)(p^0 -E_p)} \tag{2}$$ and so there are poles at $\pm E_m$.
The standard way of dealing with such an integral is of course to use Cauchy's residue theorem and choose a contour across the real line with small semi-circles of radius $\epsilon$ around the poles and then sending $\epsilon$ to zero in the limit. Thus no matter what contour we choose we should get the same answer.
What I am confused about is why we do not send $\epsilon \rightarrow 0$ when calculating these propagators. Since we do not do this we get different values for the integral (which depend on the choice of contour and how whether we push the poles above or below the real axis) and hence different propagators (advanced, retarded, and Feynman). I understand that the different propagators correspond to different supports (in terms of time), but unless we take $\epsilon \rightarrow 0$ we're no longer solving for $\langle 0 \mid [\phi(x), \phi(y)] \mid 0 \rangle$ but rather a modified version of it. What is going on here?
EDIT: To make things clearer, my question is the following: shouldn't the answer to (2) give rise to the same propagator in the limit $\epsilon \rightarrow 0$ regardless of what contour is used?