This is a non sequitur. The theory of quantum mechanics is maybe completely understood by a handful of physicists on this planet, but that doesn't mean it is full of holes; it simply means it is more involved than the average joe understands.
Major correction -- quantum mechanics is not completely understood by anyone. First, there is still no reconciliation of quantum mechanics and gravity, which is necessary for Grand Unified Theory. Moreover, even assuming a GUT is found, our understanding of what we know about quantum mechanics as far as we know it is incomplete.
Physicists do not know which explanatory model of the observed data regarding quantum mechanics is true. This is an open question in particle physics of which there are several competing models. Two of the most prominent are the Copenhagen school and Bohm's rather contrived solution regarding what is going on in quantum physics. Fact of the matter is, reality is stranger, more varied and intricate than we often postulate. There are lots of places where our understanding is clearly limited. This does not mean that God is to be found in those gaps.
In Christian tradition, God is to be found in the everything -- the idea of immanence -- the rules and laws of nature are not self-explanatory, meaning that there is no logical reason why they have to be as they are and there is no logical reason why we, from an evolutionary standpoint, should be able to understand them. Thus, you have some pretty big brute facts that must be dealt with without explanation (apparent human rationality, apparent human freewill, the apparent comprehensibility of the cosmos to human rationality and the apparent fine-tuning of the laws of nature to allow beings like us to evolve-- the anthropic principle). These brute facts can only be assumed by science, can't be proven or explained, never will be able to either -- they are epistemic and ontological problems that are not soluble within the scientific method, they must simply be taken for granted. Theism creates a framework wherein these apparent facts are understandable. Remember, if the reductionists are right, there is no such thing as free will and there is concomitantly no basis for believing humans are rational.