It is sometimes said that when science and theology conflict, this is because we are dealing with bad science or bad theology or both bad science and bad theology. This may be in fact true of a number of apparent conflicts between science and theology.
But even if this is in fact true, one shouldn't elevate such an observation into a necessarily true principle. Here is one reason to think this. We learn from history that good science is often wrong. (Can one say the same about theology? That may depend on whether one restricts to the theology of a true religion, and on how speculative one allows theology to be and still count as "good".) Unless science and theology have completely logically disjoint subject matter, so that no proposition of science can possibly entail or be incompatible with a proposition of theology, it seems quite possible to have a case where a proposition p is such that (a) p is good science, (b) p is false, and (c) not-p is good theology.
Objection 1: Science and theology have completely logically disjoint subject matter, and hence it is impossible for a coherent proposition from one field to entail or be incompatible with a proposition from the other.
Response: This is false. For instance, Christian theology holds that the tomb of Jesus of Nazareth does not contain the body of Jesus of Nazareth. This proposition and its negation are certainly the sorts of propositions with which historical sciences like archaeology deal. For another example, Jewish and Christian theology holds that the cosmos was created a finite amount of time ago. This theological proposition entails the claim that the cosmos has only finite age, a claim within the competency of cosmology (Aristotelian cosmology denied the claim; Big Bang cosmology affirmed the claim; some recent cosmologies deny the claim again).
Objection 2: Only true conclusions of science count as good science.
Response: This is implausible. Newtonian physics was good science par excellence, but false. Relativity theory and quantum mechanics were (are?) both good science, but we now know that they are not both true, since they conflict. But if this is true, then by the same token we should stipulate that only true conclusions of theology count as good theology, and then the claim that there can be no conflict between good science and good theology becomes tautologous. That said, it may be that some who make the no-conflict claim do mean it to be tautologous. Tautologies can still be useful at highlighting things—and, besides, one can't dispute them, which is certain a good thing.