Oh there are many examples of this throughout science.
In my own area (machine learning), a decade ago there used to be a huge clique of researchers who's "consensus" was that ANNs were dead, SVM+kernel methods were superior, and that few other ML techniques mattered. Actually, the problem was simply that they were training ANNs improperly. Later researchers showed how to properly train ANNs, and the work of the Toronto machine intelligence group especially established that ANNs were quite superior to SVMs for many tasks.
In econometrics, subsequence time series (STS) clustering was widely thought to be a good approach for analyzing market movements. After decades of work and hundreds of papers on this technique, Keogh et al showed in 2005 that the results of STS clustering are actually indistinguishable from noise!
Another one, in physics, was pointed out by Lee Smolin in his book, The Trouble with Physics. In string theory it was commonly, but wrongly, consensus opinion that Mandelstam had proven string theory finite. Actually, he had only eliminated some particular forms of infinities. The work on establishing string theory as finite is still ongoing.
ANNs were dead, SVM+kernel methods were superior, and that few other ML techniques mattered. Actually, the problem was simply that they were training ANNs improperly.
Well... I suppose that characterization is true, but only if you allow the acronym "ANN" to designate a really quite broad class of algorithms.
It was true that multilayer perceptrons trained with backpropagation are inferior to SVMs. It is also true that deep belief networks trained with some kind of Hintonian contrastive divergence algorithm are probably better than SVMs. If yo...
In my article on trusting expert consensus, I talked about the value of having hard data on the opinions of experts in a given field. The unspoken subtext was that you should be careful of claims of expert consensus that don't have hard data to back them up. I've joked that when a philosopher says there's a philosophical consensus, what he really means is "I talked to a few of my friends about this and they agreed with me."
What's often really happening, though (at least in philosophy) is that the "consensus" really reflects the opinions of a particular academic clique. A sub-group of experts in the field spend a disproportionate amount of time talking to each other, and end up convincing themselves they represent the consensus of the entire profession. A rather conspicuous example of this is what I've called the Plantinga clique on my own blog—theistic philosophers who've convinced themselves that the opinions of Alvin Plantinga represent the consensus of philosophy.
But it isn't just theistic philosophers who do this. When I was in school, it was still possible to hear fans of Quine claim that everyone knew Quine had refuted the analytic synthetic distinction. Post PhilPapers survey, hopefully people have stopped claiming this. And one time, I heard a philosophy blogger berating scientists for being ignorant of the findings in philosophy that all philosophers agree on. I asked him for examples of claims that all philosophers agree on, I responded with examples of philosophers who rejected some of those claims, "Ah," he said, "but they don't count. Let me tell you who's opinions matter..." (I'm paraphrasing, but that was what it amounted to.)
I strongly suspect this happens in other disciplines: supposed "consensuses of experts" are really just the opinions of one clique within a discipline. Thus, I tend to approach claims of consensus in any discipline with skepticism when they're not backed up by hard data. But I don't actually know of verifiable examples of this problem outside of philosophy. Has other people with backgrounds in other disciplines noticed things like this?