Here's a pair of arguments dear to the heart of atheists which I think cannot be consistently used together. One of them is the god-of-the-gaps objection to various theistic arguments like the argument from design. According to the GGO, finding an explanatory gap for the naturalist is not the same as refuting naturalism. Further evidence may come in which shows that the gap in question is not a real gap at all.
The other is the argument from evil. What the argument from evil points to is the fact that some evils are unexplained from the point of view of theism. There is, as it were, an explanatory gap for the theist, something the theist can't explain. Now how is it possible for atheists to use the argument from evil against theism, but then use the god of the gaps objection to theistic arguments. If a gap is fatal in the one case, it should be fatal in the other. If the gap is nonfatal in one case, it should be nonfatal in the other. What gives?