As it is explained in the "readme" part, in this specific context, "naturally occurring" means that no one has purposefully manipulated any of the images to make them collide: that the images were already published and "out there" and happen to collide. In other words, it does not necessarily imply that the images correspond to natural photographic scenes (which seems to be your interpretation of it).

Besides, you could probably "naturally" obtain such type of colliding images by photographing similar-looking objects against a white (or generally featureless) background. Furthermore, it suggests/demonstrates that similar-looking images with similar backgrounds can lead to unexpected collisions in practice (i.e. "naturally"), even if you do not assume an adversarial scenario.

Are you sure that, if you take a picture of a naked body part, it won't collide with anything that looks similar in their database?