Keep in mind that the Gemara is talking about the bumps of the spine, not its make-up.
The Gemara says that the 39 Melachos are learned from the 39 times that the word Melacha shows up in the Torah. The Gemara then asks about the word Melacha that appears by Yosef. Then the Gemara says, why don’t you simply count it up and see if you get 39 without it. Well, the Gemara says, there is also another Melacha in question — Vehamelacha Haysa Dayam — and we don’t know which one to count. By Yoseph it might not mean work, and by the Mishkan it might mean the product, rather than the work.
What we see here is that if not for the question that the Gemara had about which one not to include, the Gemara would never have mentioned why that Melacha is different. We would have been asking how come there are more than 39 appearances of the word Melacha. Some Meforshim would take certain ones out of the count and WolfishMusings would have laughed at them.
Chazal say that Yetzias Mitzraim is mentioned fifty times in the Torah. If you count it you can find almost double. There are a few Peshatim about which ones to count, but the main point is that Divrei Chazal have to be learned and studied and understood after toiling over their holy words.
The Gemara in Shabbos quotes Reb Yochanan that you may not say Torah unless you are completely sure that it is the case. He punished a Talmud for not accepting a Drasha that, to us, sounds like out of the hat.
The Maharal says that someone who knows that he is far from the Chachamim is at least on the same track, that he can realize the contrast. However, one who takes their words lightly and thinks he can critique the Chachamim is not on the same track. He doesn’t begin to understand the framework.