bike shop said bearing are ok but replaced cones.
Had to tighten the threaded axle as it was spread to wide.
OK, bearings cost like $2 a set. If the cones need replaced, bearings definitely need replaced. Old bearings with new cones mean your new cones are going to get destroyed quick. Hopefully the second part meant that they just returned the wheel to you and you put the wheel in your bike. If they gave you a bike back where the wheel wasn't tightened down, or if the rear dropouts fit properly before, but were too wide after you got the bike back, they didn't assemble it right. That's some shady bike shop stuff going on there.
If the freewheel made noise before, they could have sprayed some WD40 into it. I've actually done it before, and it does quite down the hub a lot. If you have disc brakes, and they aren't working as well as they did before, they did this, but they were very sloppy about spraying the hub and not cleaning the rotor.