The cluster decomposition principle is an interpretation of the factorization of the S matric for separated reaction :
if S_{\alpha_1,\beta_1} corresponds to the amplitude for \alpha_1\rightarrow\beta_1
and S_{\alpha_2,\beta_2} corresponds to the amplitude for \alpha_2\rightarrow\beta_2
then S_{\alpha_1\alpha_2,\beta_1\beta_2}=S_{\alpha_1,\beta_1}S_{\alpha_2,\beta_2}
Each label indicates a specification for all particles in the initial (final) state, including momenta, spins, particle species, and anything else relevant to fully specify a particle state.
Now in an EPR-type experiment, we do not have independent reactions. We have only one final state which is not separable. Since we already cannot separate the state in QM, we have no reason to attempt to separate it in QFT and hope to get a sensible result. The problem is not with the cluster decomposition principle. The problem is with the thought experiment itself. It is generally necessary to assume that all relevant quantities are measured both in the prepared initial and the detected final state.