This one really IS a controversy. On the Indonesian island Flores, inside a cave, bones from a number of humans from some 12,000 to 95,000 years ago have been found. "Human" here is a broad term including neanderthals down to modern homo sapiens sapiens. These particular bones are significantly smaller than those of other homo sapiens of the same time, and most archaeologists/biologists believe they're of a new species and call them homo floriensis, familiarly known as Hobbits. A number of scientists remain unconvinced; they point out that these could've been an isolated group of dwarf homo sapiens. Only time will tell which hypothesis will win out and become the accepted theory.
UPDATE: See this article for more details on the controversy.