As someone that was there and started blocking the SU Crit tag because of so many bad faith accusations, yeah I think I can say a bit of what happened. Might be a bit disjointed but these are the things that I remember happening.
First thing was the release schedule. The Steven Bombs. Releasing like five episodes in one week and then nothing for months. This was something that CartoonNetwork had control over and might have been something that they tried to use to get Steven Universe to stop being so popular because it was gestures pretty queer.
If Steven Universe was a show that every episode was a stand alone, this wouldn't have been an issue, but it was a linear story. So major developments could drop; major character reveals/fuck-ups could happen and then the fandom would just sit on those for months. Instead of getting the next part of the story that resolved whatever just happened the fandom could sit there and stew in theories and emotions. So characters messing up would be blown out of proration and the resolution wouldn't feel like it actually enough effort on the one that messed up end.
One example was Cry for Help. When Pearl tricked Garnet into fusing more often. If I remember right, we didn't get to Pearl and Garnet actually talking out what happened there until months after the fact. In story not much time had past but for the audience that was plenty of time for people to be offended on Garnet's behalf and distort what happened.
Anther issue was "Gem Harvest" dropped right around the 2016 election. You know when Trump became president. This was made long before the election, but there were people who took that timing as somehow Rebecca Sugar and the Crew saying stuff that they weren't. I would also say this was when the discourse really took off. If that episode had aired when the crew thought it would, probably a year or months before then, I don't think people would have misread it was much as they did. It was about communication and also Uncle Andy is the one that had to realize that the way he acted had caused him to be isolated from his family. This wasn't Steven had to "make his racist uncle no longer racist all on his own" but "Steven gave him encouragement that it wasn't too late to change". But the timing was terrible and the Crew had no control on that. The Steven Bombs made several seasons last for years when they should have been over in some months.
Second, studio interference that fandom blamed on Rebecca Sugar and the Crew. The scheduling, the ending of the show feeling rushed; those were things that parts of the fandom blamed on the crew not the network. There were people that I recall saying that the crew just needed to change how Steven Universe was written to fit with the bomb format better, when the bomb format wasn't something that the crew ever wanted. That wasn't the show style that they were telling. The show got axed because Rebecca Sugar and the Crew wouldn't drop the wedding. They wanted it there because it was important to have in a kid's show. But because they stuck to their guns the rest of the story had to be speed up, and people thought that the crew should have written the ending better; when that ending was planned to have at least another season, not a week long set of episodes. Steven Universe was set up to be a long term story. One that gave time to each character to unpack their mindset and issues. But they couldn't do that with the Diamonds.
Third, people not understanding the theme of the show. Steven Universe was about family, emotions, and open communication solving issues. Characters resolved their issues by talking about them. By being open about what the issues were. That was the reason Gem War happened; because open communication because Pink Diamond and the other Diamonds just couldn't happen. We see that Steven is at his worst when he bottles up his emotions or refuses to talk about an issue that he knows he has. But despite this theme by the time we got to Change Your Mind, people were cheering for the idea of Steven shattering the Diamonds. Which ignores the theme of the show; communication. There were people that wanted Steven to kill the Diamonds when this wasn't that type of show. Steven always hated when he couldn't talk to another character and had to bubble them. Why would this kid resort to killing? That goes against the themes of this show.
Fourth, the rushed ending. The events of Change Your Mind, was something that the crew wanted to be its own season. I imagine that if the crew had gotten what they wanted we would have spent more time on Homeworld with Steven getting to know the Diamonds and sorting out their issues. Blue Diamond would have been first since we had set up with her character first. We saw her living with the regrets of losing Pink Diamond and now not doing her duties as a Diamond. But because of how rushed the ending had to be at that point the audience didn't get that time that they had wanted. Think about how long Lars's arc was. That was several seasons long. If they had gotten a season with the Diamonds like they wanted people probably wouldn't have thought that the ending was rushed.
Fifth, bad faith criticism and very toxic fandom. As I said I blocked the SU Crit tag because after a certain point people would take anything and start shoving completely off the rails criticisms at the show and expect everyone to take them in good faith. Like people claiming that Sugar, a Jewish creator, was a Nazi Apologist because Steven didn't kill the Diamonds. People projected things onto elements of the story that weren't there. People would take a screen shot and call it lazy animation because a character was off model for a fraction of a second that wouldn't be noticed without slowing it down. There was a lot of bad faith criticism. Some of it was probably from people that didn't like how queer Steven Universe was and hid it as saying it wasn't progressive enough. There were probably people that thought that a kid's show was actually not progressive enough without looking at everything behind the scenes that the creators were dealing with. There were fans that drove one of the story-boarders/writers off the show because on her own Twitter account she posted shipping art of two of the characters (Lapis Lazuli and Peridot). It was just one member of the crew showing that she liked the dynamic between two characters that was not cannon and people started harassing them. There was a lot of entitlement from the fandom.
All of those things combined just made for a terrible time.
TL;DR: The show schedule being all over the place, studio interference, people not understanding the theme of the show, the rushed ending, and a toxic fandom with bad faith criticisms all led to the show having the worst reputation. I would say that the show schedule and studio interference played the biggest part of it since other parts stemmed issues that those created.