What are episodes from any series where you have problems with what the show presents as the correct side in an ethical dilemma.
This is a different question than purely having problems with ethical choices made by the characters themselves, as this question rests on what the writing frames as "correct" in the end.
I have two to start. The first is TOS 'Let That Be Your Last Battlefield'. It's the episode with the black and white characters locked in a constant struggle. The message is that holding eternal grudges and especially in the dimension of racism is wrong and self destructive. That's fine as it goes. The problem for me is that Kirk, and the writing frames each of the two fighting aliens as being equally at fault.
One alien is from the previously oppressive class, and is hunting down the other alien.
The second alien is from the previously enslaved class, and is being hunted.
These are not equal positions. Clearly one side is more correct than the other. Also that more correct side is being hunted, and there is no indication he is intending to continue the conflict except for when the alien hunting him catches up with him and forces another fight.
Good initial message, terrible execution.
The next episode that has never sat right with me is Voyager's 'Critical Care'. In this episode the doctor is taken to work on hospital of an alien planet where medical care is allocated by a bureaucracy that largely follows an algorithm for assigning resources. Those who are deemed more essential receive higher quality care, and those on the bottom rung get scraps.
The message about unequal treatment, and the heartlessness of bureaucracy, especially medical bureaucracy is on full display. Eventually the doctor forces medication to be distributed for all.
Seems fine as messages go, but this episode sticks in my head. The thesis of the "correct" side of the dilemma seems to assume there actually are enough resources for everyone, and I'm not sure if I buy it. Sure, showing a sliver of high ranking people getting double doses of preventative medication while the lower rung masses get nothing is awful, I wonder about the math. If 10 high ranking people are getting double doses, and you have 100 people down below who need them, then I suppose you can cut the double doses and treat 10 of the lower rung people, but you still have to exclude 90 of them. In that case, a logical algorithm to decide which of those 100 people is the best return on investment seems cold but needed. A hard choice, but the alternative is chaos. In the end, the Doctor didn't provide a roadmap for a better system, he just left the ship in the hands of a doctor who might game it for more resources, but those would logically be pulled from a central pool and leave less savvy off-screen hospitals with less. Assuming of course there weren't infinite medical resources being hoarded in the beginning. I don't know, it was just a little too murky for me.
The episode actually goes out of its way to present the system as merit based, with some of the people receiving treatment being experts in [scifi thingies]. One of the first things the Doctor tries is forging academic certificates for lower level patients to raise their treatment scores. While the episode has the atmosphere of the rich and connected being treated at the expense of the working class, its written details don't follow.