But was it a tiny-brained dwarf buffalo?

It's a short piece by John Noble Wilford, and there may be little more to say:

Remains of the extinct dwarf buffalo were found 50 years ago in a cave on Cebu, an island in the Philippines, but were not brought to the attention of scientists at the Field Museum in Chicago until recent years. They determined that the animal, which they named Bubalus cebuensis, weighed about 350 pounds and stood only two and a half feet at the shoulders.
The researchers were unable to date the fossils but thought it unlikely that they were more than a few tens of thousands of years old. A different species of dwarf buffalo lives today on Mindoro Island in the Philippines. But at 500 pounds, it is large compared to the extinct Cebu dwarf.

I find the biogeography of the Philippines and Sulawesi to be fascinating. Some mammals got there (notably pigs and monkeys on Sulawesi), while others didn't -- even those that you might expect to have because they are on Java and Sumatra. There are endemic buffalo in the Philippines now (notably the tamarao). It seems interesting that the buffalo of Java are feral, and there the native large bovid is a species of cattle, the gauteng.

I guess the thing is that there were dispersal barriers besides water in the region, so that even dispersing animals did so within relatively limited ranges. Geology is not the only answer with respect to these dispersals, and that is a lesson that is very relevant to the Flores case, although not in the way that Wilford points out.