Pointing out instances where either Chazal themselves, or Raboseinu Rishonim vaAcharonim were wrong in scientific knowledge is not necessarily denying their greatness, unless one specifically wishes to do so. In that case, it is being mevaze Talmidei chachomim and one is deemed an apikores.
If the goal is NOT trying to prove them wrong for its own sake, or to aggrandize one’s own superiority, one may actually be doing something correct. You do not need an obscure Midrash to see that some information is at odds with reality, or that Chazal themselves have admitted that their knowledge was faulty. This, latter fact is of incredible value in this argument, because, had their scientific knowledge been obtained strictly from the Torah, they would have never changed their minds to agree with the Greek or the Roman scientists of the day. When Rabbi and Antoninus were discussing the motion of the sun (in Sanhedrin), Rebbi admitted the Roman to be in the right. Had Rebbi’s knowledge stemmed strictly from the mesorah, he would have had no right to admit that his reasoning was incorrect. There are great many examples of our sages’ acceptance of the words and arguments of the gentile scientists. Even stronger is the argument that many a time when they admitted the scientist to be correct, that very information that they did agree to was later disproven as well. Had their secondary stance been derived from the Torah alone, how could have it been so patently proven wrong later?
Yes, Chazal tell us that ALL the wordly knowledge is contained in the Torah, and we must and do accept that as a fact. However, that does NOT mean that Chazal themselves understood every scientific fact and nuance thereof from the Primary Source. They knew that it is alluded to therein, and that one COULD obtain that information from the Torah, yet, they never claimed that THEY actually had all of it revealed to them. Their humility and love of truth wouldn’t allow for such statements. It does no service to the honor of Chazal to state that they were correct even in their obvious mistakes, let alone that these mistakes are actually Torah based truths.
When it comes to latter day sages, their scientific knowledge was even more derived from the gentile world, with all its wrongful facts and assumptions. Many Rishonim maintained that the Earth is flat, as Rashi interprets the Gemara of mayim shelonu, and Rashi himself, in Asara Yuchasin states that Tigris and Euphrates flow from south to north, deriving that from a posuk regarding “nahar yotze me’Eiden”. (There exist very long debates on the topic of these four rivers. How can anyone say that the Rishonim KNEW what they are from the Torah-based geography, when they debate whether one is the Nile or Ganges, with each side bringing proofs from the pesukim AND geography?)
There were rishonim that believed in warewolves, mermaids, sirens, and other non-existant creatures. Rambam quotes almost verbatim from Galen, whose knowledge of human anatomy was in fact derived from dissecting apes, and who was proven to be absolutely wrong, after 1400 years of blind acceptance. Let’s not forget the famous debate between the Rambam and the Ramban as to whether the Moon is a heavenly body or a mere apparition. Whether one wishes to rely on Mr. Armstrong’s footprint or not, one is wrong and the other is right, since their statements are mutually exclusive. This has nothing to do with the age of the Universe, or the Big Bang, and it is not as easy to dismiss as spontaneous generation of lice, which one can tweak into meaning “Chazal’s interpretation of having a spiritual existance”. Even regarding Sheidim and witchcraft, the Rambam disagrees with Chazal, stating that these do not exist, even if explicitly mentioned in the Mishna and the Beraisa.
Our reliance on Chazal as the final arbiters of Halacha, which WAS transmitted from Sinai, doesn’t depend on their knowledge of science, geography, or astronomy. The halachos of Kiddush HaChodesh are independant of existance of the Crab Nebula, or of the fact that the Zodiac is in reality NOT a set of 12 constellations, but only appears alligned as such. Ascribing to our sages infallibility in natural sciences in the face of obvious errors only detracts from following their halachic rulings, since one may begin to feel that if they were wrong in factual matters, they could have easily been wrong in halachic ones, too. Just as our respect for the Rambam isn’t due to his being a great physician in his time, but on his knowledge of the Torah, and there is no inconsistancy in accepting his psak while acknowledging his mistakes in medicine and astronomy.
Studying science reveals to us the magnitude of Creation and the greatness of the Creator. Only those who are afraid to shake their own self-serving values would continue to postulate that whatever wrongful information was sated by Chazal must be accurate, despite obvious facts. Yet, is it really self-serving? The only gain is that one ascribes to the greatest chachomim his own mediocrity and feels a need to emphatically state that those who seached for the truth didn’t.