In the story, the flatulence from the alien's sphincter is an integral part of its language (it used both orifices to communicate, and the noises it made with either orifice were incomprensible without the context of the noises made by the other).
The humans (or human) attempting to establish communication with it don't understand this, and dismiss any noises that don't issue from its mouth (or the orifice in its head) as irrelevant when trying to learn its language. This leads them to doubt its species is even sentient (iirc it may not have had clothes or tools they recognized as such either which would also have been part of it).
It may have been a short story rather than a novel.
I think I recall reading it either in the 90's or 80's (it most certainly wasn't written in the 00's).
It was definitely set on an alien planet rather than on earth.
I've a vague idea there might have been birds with four wings on the planet it was set in.
It may have been written at least in part from the aliens perspective.
Does anyone have any idea what the story I'm trying to remember is?