"They'll never let you command a ship in this condition!" (In female body)
"She couldn't be happy being...only a woman."
There was also that one with Zefram Cochrane where they determined the entity was female by its 'feminine' behavior patterns, to which Cochrane was horrified. That was just plain stupid.
Also, TNG - The Host. DS9 made the Trill into an equal relationship between host and symbiant, but in The Host is was blatantly slavery.
In The Pale Moonlight is an interesting conversation. By Star Trek morality it's obviously wrong. But it also saved about a trillion lives and preserved the entire Federation way of life.
If you found out tomorrow that the Pearl Harbor attack was actually carried out by England in order to get the US into the war, how would you feel about that? (What if you were Jewish?)