The answer to your question lies in understanding the Rambam’s Hakdama properly. The Rambam doesn’t say that there can be no loss of Mesorah. He says that when there is a machlokes, it cannot be that one side had the right mesorah and the other side heard wrong, because he would not say it as a vadai if he were not 100% certain about it (it would be an insult to Chazal to say that they would do so), and if he were uncertain and his opponent was certain about his mesorah, he would immediately accept his opponent’s mesorah. Rather, a machlokes arises when BOTH sides have lost the mesorah and they each try to recreate it from drashos, or from svara, or from diyukim in what their rebbe said.
But when a halacha is stated as the unanimous opinion of Chazal, or by one Tanna or Amora without dispute, it is almost always a mesorah.
For this same reason, when a scientific fact appears in the Gemara without dispute, such as the interval between one molad and the next, or the treifos, it is clearly a mesorah. The Rambam’s same rule applies here: it would be an insult to Chazal to say that they would state something as a fact when they were really uncertain of it, or were actually relying on the scientists of their time.
But of course there are other matters of science on which Chazal themselves disagree (such as treifah yoledes, or the water cycle), and then we can definitely say that they had no mesorah and they intended their words to be taken as svara only, not absolute fact.