Whether or not Sir Arthur Conan Doyle was actually involved in the Piltdown Hoax, his hostility toward the idea of human evolution was well known. In addition, his book, [The Lost World](https://en.wikipedia.org/wiki/The_Lost_World_(Conan_Doyle_novel) (1912) demonstrates how the author preferred to think of fossil evidence of what some regarded as past, extinct life forms; namely, that the prehistoric past was foreshortened and that humanity co-existed with all sorts of things including dinosaurs and "cave men." Doyle's frame of reference - which he bestowed on his famous fictional detective - would have placed Neanderthals and all other "troglodytes" into a recent past, thinking of them as crude, "primitive" forms of humanity occupying the land until the nobility of the "Anglo-Saxon race" arrived on the scene.

Only in that certain caves provided signs of Neanderthal occupation. So if one can deem this a "neanderthal dwelling" (keeping in mind it had also been a dwelling place for modern humans, in the 40,000 years since the neanderthal's extinction), then such a thing was indeed known to exist. Doyle wrote Hound of the Baskervilles in 1901/1902, by which times various Neanderthal sites and fossils had been identified. However, the simultaneous coexistence of homo sapiens and homo neanderthalensis in Europe had not been established, at this time. Furthermore, modern dating methodologies had not been introduced, and so the age of these fossils could not be accurately estimated. What and when precisely neanderthals were (e.g., phylogenetically or historically, with respect to modern humans) still remained a bit of a mystery.

Do you have a text excerpt? Neanderthals were not mentioned in "The Hound of the Baskervilles" as far as I can find or remember. There are references to neolithic dwellings or stone houses in the swamp, but they are not the same as neanderthals. There are definitely neolithic dwellings (4000-2500BCE) all over the British Isles and Ireland.