An excerpt from the story:

“We conducted our own study with experts in mathematics and statistical analysis, and those experts, looking at far superior data that included 148,000 calls, concluded unequivocally that there was no racial bias in officiating,” Litvin said. “You cannot use box scores to do a definitive analysis of whether race affects an individual action. We have the information on specific referees and the specific calls they made, and they don’t.”

The particular issue is that the study didn’t have access to which ref made which calls. In other words they used the racial composition of the ref crew as a guide to the number of calls. It’s an interesting point, but it’s also not surprising that the NBA would take issue with this. It is, of course, interesting that the NBA studies these things without outside prodding. Not sure what to make of that.