The majority of Achronim state that Chazal did not go by the scientific knowledge of their time.
The Rama in Toras HaOlah (1:2) states clearly that we assume rabbinic science to be infallible, and ancient rabbinic knowledge of astronomy complete. The Ramah has stated that we do not pasken like the Rambam here. As do the Maharal and the majority of our Torah authorities throughout the ages, as mentioned above.
Chida (Shem Hagedolim: “Seforim”:5:82) – There are a minority of Gedolim among us who disagree with Chazal because of their scientific knowledge, but they do not understand that Chazal had Eliyhau Hanavi informing them, and they had Ruach HaKodesh to inform them.
Maharal (Ber Hagolah 6) explaining why Chazal sometimes seem to contradict what science says:
[Chazal] [physical] descriptions, but rather the words of our sages refer to the essence, and have no relation to the outer, material matter.