Again, the article does not claim that no rapes occurred:
The question has never been whether individual acts of sexual assault may have occurred on October 7. Rape is not uncommon in war
It argues that the NYT violated its editorial standards, which is an entirely different question.
It also tries to cast doubt on Cohen’s eyewitness account, but I find it unpersuasive. First it points out that Cohen said “The terrorists, people from Gaza, raped girls” but only described one incident. Big deal. This was not a deposition. People often generalize, especially about shocking things. People say things like “Putin kills his political opponents” and “Trump rapes women” even if they only know about Navalny and Carroll.
It also points out that Cohen’s companion saw a woman stabbed whereas Cohen saw a woman raped and stabbed. Again, unpersuasive. They weren’t shooting a documentary, they were hiding. It’s entirely possible they saw different parts of an event, or even different women. If you read eyewitness accounts of the Parkland shooting you will find that not everyone mentions the exact same details, but that certainly doesn’t mean they are liars.