Strictly just pasting it into a song and selling it wasn't legal (presumably after this went viral somebody paid Trent Reznor a bunch of money and put his name in the metadata to avoid nasty legal consequences) but everything up until selling it was legal, all the raw PCM data you'd want to take the samples apart without painfully cutting it out of the entire Ghosts recording was uploaded with the Ghosts I-IV album as CC-NC-BY. This is how our culture was _supposed_ to work if we weren't still trying to find ways to put more money in The Man's pocket.
Because that example is a really weird grey area. The label didn’t clear one of the most obvious samples of all time. The original artist did not prevent them from releasing the derived work, but Tribe didn’t get paid for one of their classics.
I’m not sure what to think of that story.
The music metadata situation is pretty bad, but the source of the problem is not really carelessness or greed or avoidance of responsibility (although those are all true). The true source of music metadata complication is the insanely complex copyright regime that music operates under. It's a legacy codebase about a century in the making that is constantly being patched up by congress, mostly by trying to change who is being protected from whom. (Among the folks favored at different times: labels, publishing companies, performing artists, song writing artists, radio stations, streaming music services, live venues, ...).
Perfect compliance with these laws is effectively impossible, so everyone is just doing the best they can. And any attempts congress makes to change how things work end up being gigantic legal battles because it's a zero-sum game and the more money in the "right" hands (e.g. these artists being ripped off) is less money in the other "right" hands (e.g. the unprofitable streaming service we all love).