And they used sonic 3 stuff in Generations.
Aside from the Big Arms boss fight, it's all Sonic & Knuckles stuff. I mean, Sky Sanctuary is iconic, but you picked Mushroom Hill over Icecap or Angel Island? Yeah right. And where's my Sonic 3 soundtrack? They've released one for every other major game.
Basically, some years ago some people on Sonic Retro and VGMDB were trying to contact all the Sonic 3 composers to see who had composed what, since Sega has never released any sort of tracklist (even the S3&K tracks on the Sonic Generations soundtrack are just credited as "Sega" despite every other track having real people named as the composers). Howard Drossin was easy to contact, of course, but the Sonic 3 people... not so much. Brad Buxer was kind of an asshole about it, despite him freely speaking of it mere years earlier, and I'm pretty Bobby Brooks went off the handle and threatened to sue anyone who even mentioned Sonic 3 to him (hence why I always specifically mention him, even though he's not the only one at fault). Grigsby and Cirocco were both reluctant to speak, but Cirocco was at least nice enough to explain that there was a big lawsuit going on (and I'm pretty sure he was the anonymous source who tipped some people off about the truth behind MJ's involvement). Basically, Sega never payed any of the MJ-related people for their compositions. So... yikes.
And I mean, come on, they replaced some of the tracks in the '96 PC release, they've always known they were doing shit. So yeah, it's pretty much all their fault, and I've edited my comment because I really shouldn't be so harsh on Brooks considering he and the others were basically stolen from, but come on you don't have to be a huge asshole to people just asking innocent questions.
I'm too lazy to find sources to sight but I know Sega's ordered their composers not to ever talk about Sonic 3 (which we know because two of them broke that rule), and Jun Senoue has outright said that Sonic 3's soundtrack will probably never be released, even though Sega could easily fix this by, you know, paying up.
So in short: Fuck Sega.