Brody, 35, was accused of misgendering Caitlyn after making a remark about her transition during Monday's episode of the MTV series. "My dad, he also became a woman -- don't want to forget about that one," the reality star said. "I had been dating Kaitlynn Carter for four-and-a-half years, and my dad came out and said that he wanted to be called Caitlyn."
"Accidents happen and people slip up and you shouldn't shame them for it," he added. "There's not an ill intention."
The "I Believe" singer went on to recall the conversation he had with Caitlyn after she revealed her transition in 2015. Like his half-siblings Kendall and Kyle, Caitlyn told Brandon he could still refer to her as "dad."
"By no means am I an expert on the subject," Brandon said. "I only have my own personal experience, and in my own personal experience, this was a conversation I had with dad, which was, 'You can still call me 'Dad.' There's a part of me that relates to being your father at one point in my life, and you can still call me 'Dad.'"
He added, "So that's the understanding that we have with each other, which makes sense, so I think that that's correct."
Caitlyn has six children. She shares Burt and Cassandra with first wife Chrystie Scott, Brody and Brandon with Linda Thompson, and, of course, Kendall and Kylie with ex Kris Jenner.
During the Channel Q radio interview on Friday, Brandon admitted he sometimes feels "ashamed" of his famous last name and expressed how's he faced challenges in the music industry because of it.
"When people hear it for the first time, or they hear my last name, 'Jenner,' I think that they're quicker to write me off and not necessarily even want to give my music a chance because of it," he said. "I sometimes am almost a little ashamed of it, because I feel like people are going to have this preconceived notion that I'm just, kind of, like a spoiled kid that doesn't really have anything to say, right? And hasn't struggled in their life."
The "Death of Me" singer recalled how different his life was growing up in the years before "Keeping Up with the Kardashians" and when Caitlyn was still known as Bruce Jenner, an Olympic gold medalist.
"When I was a kid, I would hand my driver's license, or my ID, when I was younger, and somebody would look at it and say, 'Oh, are you Bruce Jenner's kid?'" Brandon said. "And they would want to shake my hand... It was this real sense of pride."
"Things have changed for me a lot,” he continued. "Just the rise of 'Keeping Up with the Kardashians' has changed the idea of what the last name Jenner, you know, what kind of person I'm going to be."