Controversy seems to be around their headline "Trump Urges Unity Against Racism" after recent gun shootings. The headline was factually correct but people are critical because it doesn't capture his slow movement on gun control and his past incitement. It sounds like lack of additional context in the headline was because of space constraints.
The editors comments in the townhall seems reasonable. They choose not to use the label "racist" because they think its more powerful to lay out the remarks in context. And the NY Times certainly seems wordy enough to pull it off.
Staffers seem very aggressive, for instance
I’m wondering to what extent you think that the fact of racism and white supremacy being sort of the foundation of this country should play into our reporting. Just because it feels to me like it should be a starting point, you know? Like these conversations about what is racist, what isn’t racist. I just feel like racism is in everything.