The core of Star Trek's Starfleet is to help promote peace and neutrality across the galaxy. When they break their own Prime Directive, it's often just to help people. It gives Starfleet quite the reputation of playing the galaxy's savior.
However, sometimes no matter how they react to the Prime Directive, they completely destroy a culture's way of living. While there might be more people singing their praises, there are definitely quite a few races with serious reasons to hate the galactic do-gooders. And no, the answer isn't Romulans (though they definitely do hate Starfleet). Here are 10 species wronged by Starfleet.
Valakians
One of Enterprise's most infamous episodes, "Dear Doctor," follows the crew helping out a species dealing with a global pandemic that they cannot solve. However, Dr. Phlox finds out in his studies that he can cure them.
This is where the problem happens.
Phlox decides that curing the Valakians himself would be disrupting the natural order, so he doesn't heal them and they just leave. After all, what if their subservient species were meant to overtake them? Therefore, he cannot get himself in the middle of their evolution.
Yes, the needless philosophy to justify by-standing in planet-wide death. So, basically early Starfleet might have willingly let this species die out.
The Edo
Fans have absolutely no clue what happened to the Edo, they can assume it didn't go well. After all, when Picard's Enterprise left, they just completely disregarded their entire justice system and way of life, despite promising to respect their culture wholeheartedly.
Why wouldn't Picard already learn the dangers of Edo laws before bringing anyone down? And why would a captain bring a dumb teenager on a first contact situation?
Even if The Edo were (hopefully) strong enough to hold their people together, they at least do not trust outsiders the same ever again. And that already destroys the overarching tranquility of their culture.
Hirogens
When Janeway made trades with the Hirogens, it wasn't really to help them in the first place. She wanted some resources and safety, and they wanted hologram technology to move away from their hunting culture. Well, safe to say just tossing the Hirogens some holodecks did not go well.
They didn't exactly give them many instructions and warnings, which led to the Hirogens making super-powered, unkillable holograms. And while they helped one Hirogen ship survive that poor choice, who knows what happened with anyone else harboring holodeck tech. They are a nomadic species, not yet at the point of collecting together. There could be in much more danger than Voyager will ever know, just because of one poorly thought out trade.
Gamma Triangulu VI
At times, Star Trek captains can be condescending and make decisions for entire cultures that they never asked for. One of the worst affected races was during Kirk's time. The people of Gamma Triangulu VI had a machine that made them young and immortal. Their lives were perfectly fine, but then Kirk helped shut its diminishing power off early, and told them to "figure it out".
Yes, very easy for people who didn't know what sex was and hadn't experienced the instinct in decades (even centuries) could easily just "figure it out".
In the best-case scenario, they changed their entire way of life, figured things out, and experienced dying and legacies. Not the most pleasant. But worst case, they were unprepared and died out.
The Ba'Ku
While Picard's crew did their best to help the people of Ba'Ku, Starfleet was less kind about it all. They were working with the enemy to remove the planet's people, just so that they could mine and destabilize the planet for its life-extending resources.
How very unfriendly and awful of Starfleet. Doesn't quite line up with the peaceful motto of theirs.
Even if they did save the planet for the Ba'Ku, they had to deal with the entire situation and the threats to their lives. Starfleet completely uprooted this entire race and changed their culture irrevocably.
Species 8472
Ultimately, its the Borg's fault that Species 8472 got released into the Delta Quadrant, and it's understandable why Janeway teamed up with the Borg to stop them short.
However, Janeway's choice (before she knew all the facts) led her to help execute many of the species that got pulled into this space-zone by the Borg themselves. This also trapped some of the poor species in this space, unable to really understand or connect with anyone around them.
Her alliance with the Borg irrevocably changed the ones in fluidic space (knowing they could be pulled across like that) and really messed up the lives of those trapped in the Delta Quadrant.
Bajorans
The Cardassian War was not an easy time, but the way Starfleet and The Federation let the Cardassians treat the Bajorans was abhorrent. Their occupation left the Bajoran people battered, angry, and bitter, and rightfully so.
Letting the Cardassians get away with that treatment for so long, all for the sake of peace is terrible. No wonder Bajorans don't really trust The Federation. Their people were left to suffer while the Cardassians took advantage of and massacred their people. They deserved better.
The Pell/ Gosis's People
Unlike other Star Trek captains, Archer and co. had a habit of going down onto planets populated by people with inferior technological capabilities. The point was to study their planets, the people, and get data on them.
However, even just being there was a constant risk that would be a direct violation of the Prime Directive in a few decades.
In one survey, Reed left his communicator on the planet. Not only did it cause a complicated incident that almost made them lose their lives, but it also completely changed the planet-wide conflict. They forever changed this species to be more paranoid and perpetuated their civil war.
The Kyrians and Vaskans
During their travels through the Delta Quadrant, Voyager ran into many different species that no Starfleet member every met before. One example was two warring races on one planet, the Kyrians, and the Vaskans. Somehow, the history books blamed Voyager for the conflict that worsened between their two people.
However, a copy of The Doctor ended up on the planet, and, after decades, a historian finally released him. The Doctor explained that the conflict was caused by the visiting races, not by Voyager.
Acting as a catalyst for their conflict, though, and the lies that followed, Voyager did make the planet worse for wear.
Organians
So, once upon a time, Klingons planted some of their people on the planet of the Organians. At the time, they were using fake corporeal forms to be received better by other people in the galaxy. When Captain Kirk and co. offered help, the Organians refused it because they didn't care. Despite their refusal, Kirk and Spock started a guerilla war against the Klingons on their planet.
To stop the two sides from warring, the Organians had to shed their disguises and use their power to force the two species to come to peace on their planet. While their intervention was great for the future Klingon and Human friendships, it did ruin the Organians cover and lifestyle in the eyes of the galaxy.
Starfleet ruined an entire species' persona just because they had to stop a fight like a parent would restrain toddlers.