Molinist evolutionary theory (MET) holds that evolutionary theory is correct and based on genuinely random processes. Nonetheless, according to MET, these processes are guided by God. For each random transition (e.g., a random mutation, recombination or selection event) has associated with it a subjunctive conditional of the form "if circumstances C were to occur, then transition T would occur". God non-trivially knows the truth values of all such conditionals, and created the world so as to ensure a sequence of circumstances C that, given the conditionals he knew, would result in a sequence of transitions that fits with his plan.
I have argued elsewhere (a version of this has appeared in Philosophia Christi) that this story undercuts the statistical explanations that evolution needs. Here I want to point out a second issue. We know the probabilities of outcomes of processes in nature essentially by looking at frequencies of outcomes[note 1]. But, almost surely[note 2], a Molinist God can get any sequence of outcomes he wants by tweaking the circumstances appropriately. If a coin is to be flipped a million times, a Molinist God can make them all come out heads not by intervening in the flips, but by ensuring that the conditions C in which the flips happen are such as to make true appropriate conditionals of the form "C→heads".
Given the existence of a Molinist God, one might expect, or so Mike Almeida has argued, observed frequencies that do not match the probabilities involved in the processes. In fact, this might even give rise to an interesting prediction: given a Molinist God, we might expect the more needy to be disproportionately represented among lottery winners, since it seems not unlikely that God would want to choose initial conditions to favor them. If this line of reasoning is right, then given the existence of a Molinist God, the frequencies we observe should not reflect the probabilities of the underlying physical processes. But if so, then our knowledge of the probabilities of the underlying physical processes is undercut. And this is surely a problem for MET, not because it falsifies evolutionary theory, but because it undercuts it epistemically, making it impossible for us to know the probabilistic claims on which evolutionary theory is based.
Suppose, on the other hand, our Molinist rejects the Almeida argument, and holds that even given a Molinist God, the observed frequencies will match the probabilities of the underlying physical processes, perhaps because God would want them to match in order to be a self-effacing creator, or to let us engage correctly in inductive reasoning. In that case, the following is still true. The observed frequencies are not directly evidence for the probabilities of the underlying physical processes. They are only indirectly evidence given some assumptions about how one expects God to act.
Here is another way to put this. On the Molinist view, there is a defeater to our knowledge of probabilities on the basis of frequencies: the frequencies come from God's decision as to the antecedents of conditionals. A controversial thesis about how God chooses to act, if substantiated, would provide a defeater for this defeater. This makes knowledge of probabilities of physical processes rather more roundabout than we think it is. Moreover, I am not clear whether on this view an atheist can know any claims about these probabilities, since God's contingent decision to make the frequencies match the probabilities seems to play a central role.