Schematically:

1) model M claims that X happened necessarily the way it did, for reasons we don't understand.

2) A critic presents a counterfactual C where X doesn't happen that way, while C is still consistent with the model. To argue that C changes X, he uses causal reasoning.

3) The defenders of the model must now either abandon the model, show that C is not actually consistent with M, or refute the claim that C changes X.

4) The conversation has now progressed beyond direct claims of likelyhood or not of M.