Let’s be real here, she started off just writing a fun story, think nothing of it, and it became a cult. There’s two ways to go about this; 1) milk it for everything it’s worth, or 2) let the fans go apeshit on fanfic without providing anything more. She chose option 1. Cause money.
Arguably I think all the flaws combined with its popularity is why there are so many HP fanfics out there and they are at least part of the popularity of the work.
It’s like confidently posting a wrong answer on the Internet, people can’t help but want to correct you. Same with her story, which fuels a good chunk of the dialogue and discussions about it.
If it was bad or unpopular no one would care. If it was extremely well written, with little to no plot holes, people would like it, but that’s kind of it. Harry Potter just seems to have the right mix of good ideas and poor execution while remaining popular enough to be relevant to generate seemingly endless efforts to fix or improve it.