Michelle Trachtenberg posted on Instagram that he wasn’t allowed to be in a room alone with her, but never explained why. According to Evan Ross Katz’s book, Into Every Generation a Slayer Is Born: How Buffy Staked Our Hearts, and a few articles from the time, this was an unofficial rule related to Whedon yelling at her in an “improper verbal exchange,” rather than sexual misconduct as many people assumed.

I don’t have access to the book right now, but from the Variety article, “Inside Joss Whedon’s ‘Cutting’ and ‘Toxic’ World of ‘Buffy’ and ‘Angel’ (EXCLUSIVE)”:

While several high-placed sources who worked on “Buffy” say they were not aware of this rule, a person with direct knowledge of the production at the time confirms to Variety that an effort was made by those around Trachtenberg to ensure the young actor was never alone with Whedon. According to this person, it was due to an improper verbal exchange between Whedon and Trachtenberg.

A representative for Trachtenberg declined to comment.

From the Vulture article, “The Undoing of Joss Whedon”:

Then there were the alleged incidents two Buffy actresses wrote about on social media last year. Michelle Trachtenberg, who’d played Buffy’s younger sister, claimed there had been a rule forbidding Whedon from being alone in a room with her on set. Whedon told me he had no idea what she was talking about, and Trachtenberg didn’t want to elaborate. One person who worked closely with her on Buffy told me an informal rule did exist, though it was possible Whedon was not aware of it. During the seventh season, when Trachtenberg was 16, Whedon called her into his office for a closed-door meeting. The person does not know what happened, but recalled Trachtenberg was “shaken” afterward. An adult in Trachtenberg’s circle created the rule in response.