Stonecore heroic was "hard" simply because the trash was god awful and there was way too much of it:
First three packs: Incredibly annoying. Had to CC one of the berzerkers, had to have a dedicated interrupt on the Earthshaker or w/e his name was (guy who turned into an elemental) and possibly Milhouse Manastorm because he just AOEs everyone. Pretty much needed to mark a kill order.
Stone Golem: Loved these guys because people are dumb and can't jump to avoid earthquakes
Rock Flayers: Loved these guys too
Room before Ozruk: Can die in a fire. Way too much trash, and extremely annoying as well. You could easily be screwed if you didn't have a Shaman to lock down the fire elementals. The big ogre guys could easily oneshot a healer if RNG was bad, since their shockwave attack or whatever didn't give you enough time to move away, and they jumped around. The summoner usually had to be CC'd just so he wouldn't spawn a million imps.
Similar thing goes for the other two "terrible" dungeons: Deadmines (also way too long, and the gauntlet was shit) and Grim Batol. They weren't hard, the trash was just garbage. Honorable mention goes to the packs with the healing Naga in Throne of Tides, the groups with Twilight Borers in BRC, the guys with the lightning grounding field in Vortex Pinnacle (some of the worst trash ever) and the groups in Lost City with the Plaguebringer and the Darkcaster.
As for the bosses, they were fine other than Ozruk having that stupid "Have to dot yourself to break" shield and the bugginess of Shatter before the graphic outlining where it would hit was added, and the idiocy on the last boss with the rocks where it could clip you even without you being in the impact zone.