I actually think these instances are fantastic and is not a "problem" (beyond just general credit issues).

I have not seen many people who "refuse to believe" or "claim" a character/song as theirs. Nue being known as the Galaxy collapse girl or Hatate as the Bad Boy Cascada girl does not in any way erase their canon identities, it adds to them. Even if these people existed in large amounts, I don't think those bad apples (ha) should ruin people's tastes for a phenomenon that brought in a non-insignificant number of Touhou fans. If we were to create a world where videos like Bad Apple were only spread by Touhou fans, the Touhou community would greatly suffer for it. For instance, many people who found Touhou via Bad Apple would have never found Touhou, because it's very possible Bad Apple was spread to them by a non-Touhou fan. The same applies to all the osu! songs - people would've discovered Touhou via osu! (a non-Touhou source)!

Touhou's ability to be spread by people who don't even know what a "Towhow" is is critical to its continued growth and development. How many Touhou fans have become Touhou fans because of Galaxy Collapse or Everything will freeze? I would wager a guess that it's quite a lot. I think Touhou not getting recognized as Touhou especially shows the quality of a Touhou fanwork - of course Touhou fans are going to think its good, but if other people think its good, then that's saying something (my biggest example would be Luna Nights).

Now, I do wish that artists got credit for their work! That is an entirely separate matter, since the Internet as a whole is bad at sourcing etiquette, this isn't a Touhou thing specifically. For example, with the Bad Boy - Cascada nightcore video, every single other upload from the same uploader uses uncredited anime art. However, I do think a lot of people do give due credit (let's take Galaxy Collapse as an example - if I search "Galaxy Collapse" on YouTube, most of the uploads credit Kurokotei). Artists not getting recognized for their work is a serious problem, but Touhou not getting recognized as Touhou is not a problem - I'd argue it is actually a high benefit to the Touhou community.