Sure. The first televised interracial kiss that was depicted in "Plato's Stepchildren" (TOS) raised a few eyebrows (other than Spock's). And the lesbian kiss in "Rejoined" (DS9) caused quite a lot of uproar, despite the conditions that were imposed to make it seem like it wasn't truly a "lesbian" kiss. I'm sure there are a few others I'm missing! Others feel free to add on.
Apparently Plato's children didn't cause much of a genuine uproar when it was released. and they only received one angry letter
I'm pretty sure when Kirk said "Let's get the hell out of here" was controverial too. (City on the Edge of Forever)
Studio executives considered the concept of the Female first officer, Number One, (played by Majel Barret Roddenberry) in the first pilot to be contriversial. That was one of the reasons why Star Trek wasn't picked up until the second pilot.