Depends on what is meant by 'emergence'. If you mean to say that 'emergence' itself is "mysterious" then I would disagree. Chemistry is 'emergent' from physics -- molecules possess attributes that their constituent atoms do not -- but no one would describe this as "mysterious". It's simply a question of scale.
Consciousness described as being 'emergent' from our neuroanatomy is hardly a 'mysterious' statement: it's simply a claim of "scale". One would not examine the exact behaviors of every atom in a molecule to predict its characteristics: no matter how much oxygen or hydrogen you have at room temperature the characteristic of "wet" would never be noted. Only dihydrogen oxide at room temperature (and in sufficiently significant quantities) has that characteristic. So too, potentially, is it with consciousness: while yes it is necessary to understand the workings of the constituent parts it is only by observing how they interact as a whole that consciousness can be comprehended -- in much the same way we would not discuss the phenotype of E.coli in terms of their spacetime tensor coordinates.
But I digress.
I am looking for examples of mysterious answers that were eventually explained *away* by science. I can think of two: One is the belief that the behaviour of living things was explained by the mysterious force of elan vital, and not by mere chemistry; which was destroyed by the synthetisation of urea. The other is the special (and mysterious) role of the conscious observer in quantum mechanics, which was explained away by demonstrating that rocks can get entangled with electrons just as much as brains can. Can anyone furnish me with other examples?
I observe in passing that phlogiston is *not* such a mysterious answer. Eliezer is down on it, but I think unjustly so; for people did in fact perform experiments on phlogiston, including the final experiment to find the weight of the phlogiston that had passed out of the burning material and into the byproducts. It turned out that the phlogiston had negative mass... in other words, that the direction of the transfer had been misidentified. But if you think of phlogiston as `negative oxygen', it makes the same predictions as modern chemical theory. This is no worse a mistake than mistaking the direction of the current, a mistake which is *still* enshrined in our sign conventions; it is not a mysterious answer of the form "X->Y" with no details of X given and any value allowed for Y.
However, I digress. Mysterious answers blown away by experiments, anyone?