Heche, 51, told Mr Warburton magazine that she hadn't spoken to Ellen in years.
"I'd listen to the people who have," she said.
And although she didn't get into the details of the scandal, she hinted that there might be truth to the claims.
"If I'm standing someplace and I don't like what's going on there and I stay there, it's my fault," Heche said.
"So what are the actions that got me there and why can't I get out of it easily if that's not something that I want to be engaged in?"
She added, "Ellen is standing where she walks, and that is hers to continue that journey."
But she did say the relationship was a "beautiful part" of her life. She dated the talk show host from 1997 to 2000.
Ellen's reputation took a turn for the worse when a tweet claiming she was "notoriously one of the meanest people alive" went viral online. More than 1000 people replied to the original tweet, sharing their unpleasant experiences with the TV star.
Countless staff then came forward with their own accounts of bullying. This forced Ellen to apologise on the show and triggered an internal investigation, leading to the firing of three senior staff.