You should read your sources more carefully:

> the first occurring about two million to 1.5 million years ago during the late Pliocene and early Pleistocene epochs; a second during the mid Pleistocene, roughly one million to 500,000 years ago; and ending with the spread of modern humans, 50,000 to 30,000 years in the past.

> The new findings, published this week in Proceedings of the National Academy of Sciences USA, casts doubt on the second migration out of Africa. "[The researchers] are not denying that it happened," Trinkaus says, "just that it was less important than movement across Eurasia."

The degree of second migration is what was brought into doubt, not that all humans today share a common ancestor from the 3rd migration.