but the article state "This interaction is controlled by turbulent swirls from the upstream dune". Are the sand dunes themselves willfully creating these swirls? Could they choose not to create the swirls?

Nowhere in the definition is intent specified. This article is hardly the only place the word "communicate" is used to describe the behaviour of inanimate objects. For example, "communicate" is a handy descriptor in gas dynamics to explain the differences between supersonic and subsonic flows. In subsonic flow, the particles can communicate with upstream particles, but in supersonic flows they cannot. This is a useful way to conceptualize the differences between the two flow types, and can help a student gain an intuitive understanding of why a wing flap that works in subsonic flow may not work in a supersonic flow without a radical redesign.

In this situation, the use of the word communicate is accurate to the definition, and also a useful tool for gaining an understanding of what is happening. The word is used because it is useful. It serves a purpose beyond anthropomorphizing for the sake of anthropomorphizing.