I've seen the accusation, but no evidence that supports it. Now, I do find many of Carl's quotes tedious and repetitive. I am inclined to skip many of them. But I have looked at Carl's quotes against the "larger context" produced by some of the people claiming he is quote-mining. (Most of the accusers don't even try to produce a "larger context.") He is not changing the meaning of the original authors' words. He is not, in the fashion of (for example) Ray Comfort, quoting a question, presenting it as unanswerable, when the author presented a question for the purpose of giving the answer. What he is doing is changing the focus. He is drawing attention (to the degree that people aren't passing over him in boredom) to things the original authors were admitting, but trying to gloss over. He is also throwing in useless bible quotes; but that is another matter.
So why the accusations? My personal suspicion is that Carl is bringing up an inconvenient fact. Scientist have not conducted experiments to try to determine whether large-scale evolution is true, but instead have assumed large-scale evolution to be true and have conducted experiments to determine which path it has taken. Some scientists openly admitted this (20 to 30 years ago) while treating it as a relatively unimportant point. More recently, they seem to be taking care not to admit that. So people can (and do) correctly claim that his quotes are antiquated. But what they can't do is produce an experiment that didn't have every outcome conceivable before the start of the experiment be one that either supports evolution outright, be a declaration of a path for evolution, or be "inconclusive." At no point was there ever a risk of a "disconfirming result."
Now, none of this should be taken to mean that I somehow support "intelligent design." I don't. If there is somehow a designer, the competence level is comparable to such fictional characters as Peter Peachfuzz and Maxwell Smart. But I don't need an explanation for the diversity of life. Nothing is dependant on it. If large-scale evolution turned out to be false (and how would anyone know?) medicine would be undisturbed. It only depends on small-scale evolution -- and specificly that later generations of bacteria adapt to the environment in which they find themselves. It doesn't even depend on the observed fact that separated populations of bacteria can become distinct species. Why do people think it is so important that everyone believe large-scale evolution is true? To me, it makes as much sense as being adamant that everyone have the "correct" belief regarding whether Sirius has an orbiting planet with a large diamond at its core. It's not going to change anything.