Unintentionally Unsympathetic / Star Trek: Deep Space Nine

• "Progress" features the Bajoran government getting ready to tap the core of one of its moons for energy (which will render it uninhabitable), and Kira dealing with one farmer who is refusing to leave the home he had made on said moon. The conflict is treated as a common The Needs of the Many scenario, but that falls apart when one examines the details. Intentionally ruining a habitable world and destroying all of its indigenous life seems an astonishingly cold-hearted decision for the Bajoran government to take, especially considering that there are famines all over Bajor and they need all the farmland they can get, and the benefits of the project (powering "a few hundred thousand homes", something any nuclear plant can outdo, and most likely a small percentage of Bajor's overall energy needs) don't seem to outweigh the costs. One can't help but wonder whether there were any other planets or moons in their solar system^note There are fourteen planets in total, and Bajor itself has five moons that would have worked for the energy project and also don't have any indigenous life forms to complain.
• "In the Hands of the Prophets" centers around Keiko's new school, and some of the Bajorans (led by Vedek Winn) taking offense to her teaching their children about the wormhole and the Prophets in a scientific context (in a not-so-subtle allegory for the creationism vs. evolution debate). As the conflict escalates, Sisko tries to get Jake (and presumably the audience) to sympathise with the Bajorans by pointing out that they have been free to practice their religion for only about a year. However, Keiko's science classes do not in any way infringe on the Bajorans' religious freedom — Sisko had previously pointed out that students could simply receive religious education separate from the secular education that Keiko provides (which is the compromise widely used in the real world). Plus there's the blatant hypocrisy of having victims of religious oppression turn around and try to censor ideas that conflict with their religion. As such, it can be difficult to see the opposition to Keiko's school as anything more than rabid anti-intellectualism.
• In "Sanctuary", The Skrreeans believe Bajor is The Promised Land Kentanna based on Haneek's interpretation of an old religious legend that Kentanna is "a planet of sorrow", and they take that to mean Bajor. The Federation offers them the planet Draylon II to settle and claim as their own, but the Skrreeans refuse because they are certain Bajor is Kentanna. When the Bajorans refuse them on the grounds they have a lot of their own problems to resolve, the Skrreeans are extremely upset. Haneek spitefully accuses the Bajorans of being paranoid and suspicious and accuses Kira of betraying her. This all makes the Skrreeans come off as extremely entitled and ungrateful, spitting on the Federation's offer of Draylon II and demanding the Bajorans take them in. It doesn't help that the Skrreeans have been largely unsympathetic throughout the episode, with Haneek's condescending misandry and the males' pugnacity.
• In "The Abandoned", Quark purchases a load of salvage which, unknown to him, includes what is later revealed to be an infant Jem'Hadar. Sisko self-righteously and incorrectly accuses Quark of purchasing a child, ignoring Quark's truthful protests that he had no idea. When Quark objects to the rest of his property being summarily seized by Starfleet, Sisko only shoots him a Death Glare. You'd think if it were anyone else, he'd be more professional and assure them that their property rights would be respected once the investigation was complete.
• "Prophet Motive" has Grand Nagus Zek show up having been mysteriously transformed from a typical greedy Jerkass Ferengi into a paragon of generosity (later revealed to be the result of him contacting the prophets trying to gain knowledge of future events, and them taking offense to Ferengi greed). Though there are moments when the "good" Zek comes across as just as much of a jerk as the regular Zek. Notably, he discards every object in Quark's quarters because it was "getting in the way" and then screws Quark out of a perfectly legitimate business deal. He doesn't seem at all concerned with the effect this has on Quark.
• In "Homefront", O'Brien discusses the recent bombing of a diplomatic conference on Earth, lamenting how frustrating it can be to see something you care about in danger and be powerless to help. Quark attempts to empathize by talking about the dwindling of his financial investments during an economic crisis, but O'Brien and Bashir dismiss it as typical Ferengi greed. Yet for someone who does not live in a post-scarcity utopia, living through an economic crisis actually can be a severely stressful experience (just ask anyone who lived through the 2008 recession). As such, the reactions of O'Brien and Bashir come off as insensitive.
• In "Profit and Lace", Ishka spends much of the episode being incredibly ungrateful to Quark about everything up until she has her heart attack. Never mind that Quark had made an honest effort to accommodate her with her feminist agenda despite personally disagreeing with it. And this is not long after Quark risked his own life to rescue her from the Dominion.