I've been suggesting for some time that the term "Borneo pygmy elephant" was incorrect, and started by the wildlife tourism industry.
The website of the Malaysiia-based wildlife and conservation NGO Hutan has an article (no date given) titled Pygmy or Just Borneo Elephant?, which opens by asking, is there really such a thing as a "Borneo pygmy elephant?" This referred to a 2003 WWF-Malaysia press release sent out on the occasion of a paper being published that identified the elephants of Borneo as part of a new sub-species. The press release used the term "Borneo pygmy elephants," which seems to have "caught on." Hutan says the elephants of Borneo should correctly be referred to as "Borneo elephants."