The scientific process, by definition, is going to yield incorrect results most of the time. It's an inductive process. The errors normally come to light when new measurements, or new information, invalidates or refines a previous view.
It's probably not the best strategy to rely on the 'can't explain X' / god-of-the-gaps argument. From a sheer strategy standpoint, theists really should stay clear of this game plan.
Theories will be refined, more information will be found, and refined again. Explanations will be formulated, applied to other aspects of life, and verified. When that happens, it does 10 times more damage to the theists credibility (regardless of which side is correct) than any atheist on a forum, spouting off names, could ever do.