I don't know if the specific data Pinker uses to make this particular case has been (is being) challenged.
There is a lot of opposition to the general ideas put forward by the evolutionary psychologists (EP's). Some of it led by the British scientist Steven Rose. There is a series of essays : "Alas poor Darwin" which is edited by Rose and his wife Hilary Rose which critique the EP's and Dawkinsian ideas. Essays by Gould, and Mary Midgely are included in the book.
I have to say that I didn't find the book had much to offer. It was a lot of polemic without (I felt) much substance. I was so disappointed I wrote a review of it for inclusion on the Amazon website, but they never used it. I kept toning the language down and resubmitting it but in the end I reached a point where my principles would let me go any further. So I sent an email to Amazon telling them what I thought of them for not including it.
I'm not sure whether Rose would thank me for describing him as a Marxist, but his views are left of centre, and I think he thinks of EP as being freindly to the right wing. (I have heard Matt Ridley described as a right-wing libertarian.)
Another strand of objection seems to be from social scientists who have been brought up in the SSSM tradition and are resistant to change. For these people EP is a massive paradigm shift.
When we went to the Simonyi "Blank Slate" lecture in Oxford, someone asked Pinker how she should deal with the old guard. And Pinker said that she shouldn't worry too much because he said (something like) "We have time on our side."
I'll post my critique in the writing centre - but not now - My wife is telling me I'll be late for my daughter's wedding.