In the Hindu Sanskrit literature of Itihasas and Puranas it is actually made explicit that Humans ("Manusya/Manava" in Sanskrit) are distinct from other beings (eg. "Devas/Asuras/Vanaras/Gandharvas" etc. in Sanskrit), each with their own specific characteristics. And also there are plenty of stories of interbreeding amongst them.
It is fascinating to note that the distinctions are pretty clearcut throughout the vast corpus which implies it was common and wellknown at that time. There seem to be some good parallels to our anthropological knowledge of different Homo species.
In particular, the "Vanaras" were a humanoid ape-like species who have all the human psychological characteristics but with ape-like physiology. This was one source of inspiration (amongst others) for the "Na'vi" in James Cameron's Avatar movies.
Those myths and legends are old enough to contain traces of shared Indo-European beliefs, so the real old stuff should be found, in some form, in other cultures, like Greek or Norse mythology. But I don't think it is true in this case
The vanaras were probably conceived of around let's say generously 3000 years ago. Neanderthals disappeared about 40,000 years ago. You live ten times closer in timeline to the original Ramayana story than neanderthals did.
It's just not very plausible that hindu mythology is a corrupted record of living with multiple species of hominids. Timeline-wise, it's not much different from claiming that Tolkien's orcs and elves were part of some kind of historical memory of hominids.