The Rishonim, upon their own admission, listened to the scientists of their day. Therefore we don’t have to accept their science, although we try very hard to do so. And we learn the Torah thoroughly and try to adapt it to updated science.
Although we know that they didn’t know the science that we know today, their Sefarim were written with Ruach Hakodesh, which doesn’t mean they were ‘told’ what to write. But it does mean that their words are Emes and have great Kedusha.
The Amoraim, on the other hand, always quote earlier Amoraim or Braysos for facts of the world. They never quote a doctor, philosopher or scientist. They did consult doctors for Halachos at that time, but Halacha was never based on a doctor (besides Shmuel).
The Gemara in Pesachim that says that the non-Jewish Chachamim seem correct (in a topic with little relevance today) shows us that the Chachamim did not get their Chachma from them. When the Gemara suggests that our Chachamim seem correct on the second issue, the Gemara rebuffs the proof to explain how the Chachmei Umos Ha’olam can be correct (also based on a premise disregarded today).
The first issue was if the sun goes over the Rakia or under the earth. This would mean that they never bothered to watch Shkia! It therefore seems most likely that it wasn’t quite a scientific argument in the first place, and as the Maharal explains it.
Anyhow, the Gemara never implies that they knew everything there is to know, but it is pretty clear that the Braysos are true and the Tanaaim didn’t just pass on their speculations. Rebbe Yochanan, who compared his understanding to a pinhole relative to a few generations before him whose undertanding was as wide as the Ulam, insisted that nothing be said until it is extremely clear.