Salamandyr
Adventurer
While I'm not certain about this specific case-assuming a vanilla, roughly 16th Century tech world which seems the default D&D standard. A scholar very well may have heard stories of some desert dwelling creature even though he'd personally never ventured there. I think people underestimate the extent to which information, if not always people, moved around in even the ancient world. There was a silk trade during the Roman Empire for instance.
However, while I may quibble with your DM's specific ruling in this case, I think his basic interpretation is sound. Not everything should be knowable just by rolling high enough on the die. I once ran a campaign with two players with very nature savvy characters. They had an encounter with a couple of dinosaurs. One of them, quickly rolled out a 35 on their Knowledge Nature roll and said "MY character identifies it". The other player rolled something almost equally high. I replied "You're pretty sure it's an elephant!" (one found this hilarious, the other was consternated I was "gimping" her character). But in this campaign, tech levels were closer to 10th Century, it a dark age, sword & sorcery world. Neither characters background involved extensive travel, or access to large cities, and archeology wasn't really a thing, so the characters high rolls only allowed them to think of a creature they could reasonably have "heard" of. The consternated player was equally consternated that another player could tell it wasn't an elephant, not because of a roll, but because the character came from an area of the world that had elephants (unlike the two nature savvy characters) and would have definitely seen them in the past.
What it came down to was, in my estmation, none of these characters were equipped to recognize a dinosaur, or to have even heard of the existence of such a thing, until they saw one, no matter how high they rolled on their knowledge nature skill.
However, while I may quibble with your DM's specific ruling in this case, I think his basic interpretation is sound. Not everything should be knowable just by rolling high enough on the die. I once ran a campaign with two players with very nature savvy characters. They had an encounter with a couple of dinosaurs. One of them, quickly rolled out a 35 on their Knowledge Nature roll and said "MY character identifies it". The other player rolled something almost equally high. I replied "You're pretty sure it's an elephant!" (one found this hilarious, the other was consternated I was "gimping" her character). But in this campaign, tech levels were closer to 10th Century, it a dark age, sword & sorcery world. Neither characters background involved extensive travel, or access to large cities, and archeology wasn't really a thing, so the characters high rolls only allowed them to think of a creature they could reasonably have "heard" of. The consternated player was equally consternated that another player could tell it wasn't an elephant, not because of a roll, but because the character came from an area of the world that had elephants (unlike the two nature savvy characters) and would have definitely seen them in the past.
What it came down to was, in my estmation, none of these characters were equipped to recognize a dinosaur, or to have even heard of the existence of such a thing, until they saw one, no matter how high they rolled on their knowledge nature skill.