I know, it has. But "holes in the theory" was never a reason to dismiss it. It's not as if there was a better theory around the corner, we could use.
For a long time it was believed that the landliving vertebrae always had five fingers and toes per hand, as today's vertebrae have at least in their embryonic phase, and there was a big hole in the theory of evolution because why exactly five? Today we know that the first landgoing vertebrae actually had more digits, they started out with eight, later we got seven, then six, and finally five. It seems that five digits is a local optimum for digits, as all subsequent vertebrae stayed with five - evolution slowly converged to it. So this hole was filled.
And so it goes with every hole that one points at. We know the process of coagulation pretty well, and we can see right now how it has evolved: the basic mechanisms are controlled by more complicated mechanisms, whose in turn have another layer of control upon them. Each layer evolved because the lower layer was prone to (deadly) errors. We know that the flagellum of Escheria coli is based on 40 proteins, and if one is missing, it won't work. But if we look at all flagellae in all bacteria, only 23 of the proteins are shared between them. So at first, we have literally hundreds and thousands of different flagellum recipes out there, which strongly hints at a random process with lots of possible outcomes. And further we know that if we throw out some proteins, we get the Type III secretion system. So even an "incomplete" flagellum was an evolutionary advantage - another hole is filled.
And so it goes - whatever hole you point at, it is already filled with some good research.
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