One says that evolution is accelerating and one says that evolution has basically stopped.
They're at odds.
One covers a time period of 50,000 years, with this key caveat by the conductor of the research:
"The technology can't detect anything beyond about 2,000 years ago".
The article from Time is only discussing the past century or two, so it's arguments apply exclusively to the time period the techniques used in the first study can say nothing about. They don't contradict each other - they're looking at different things.
It's true that at least one of the authors of the study publishing in PNAS, Henry Harpending, would disagree with the Time article. To complete the quote above:
"The technology can't detect anything beyond about 2,000 years ago, but we see no sign of [human evolution] slowing down. So I would suspect it is continuing,"
but this is his personal suspicion - he's not pretending it's established by their research.