Dinosaurs were actually the legendary dragons of yore.

They went extinct sometime near the end of the middle ages due to over-zealous young Knights hunting them to impress damsels.

The bones we find that are fossilized were made this way by Basilisks who were a natural predator of dragons and whose gaze could turn them to stone.

The reason we find these fossils in such deep strata is due to
massive quakes caused by the Giant's War circa 863 AD.

The Giant's War was removed from historical record by the Vatican by decree of Pope Innocent XI as he was attempting to preserve his title as the tallest man in the world.

Hope this helps OP.