Subject says it all. I've never once had anything sort into the junk category. If it says "Sell to merchant for gold" then it should be put there so I know to dump it
you need to right click the item and select "mark it as junk". This also allows you mark items, like duplicate recipes and sell everything "marked as junk" at a click of a button.
Common sense, so rare it's a God damn super power....
However the last time I played (see my sig) things marked as junk did not remain junk the next time you went out collecting after selling everything from that tab.
I'm having the same issue. Maybe there's an addon which fixes this for now? If not, I hope it gets addressed at some point. I don't think it's a major issue, but it is annoying at the least.