In a Season 4 episode of "Bones" there was a very problematic plot revolving around the androdgenous Dr. Tanaka, whose gender Angela obsesses over.
The Bones Scene That Went Way Too Far
One of the best things about "Bones" is the even-handed, accepting nature of the Jeffersonian staff when confronted with lifestyles they've not previously considered. The pony play episode was surprisingly respectful, the (poorly titled) episode about a trans victim worked hard not to misgender her... But one time the show just completely whiffed it.