The bikes usually come with a little pack of propaganda. Included in this pack, from Shimano, is a sheet showing the gear ranges for each chainring. #SI-FC00C, it shows the combos that you might get some rubbing in.
You can usually get them to not rub in most gears but it depends on the frame. It also helps if you have a shifter with trim. The Sora shifter has a trim position, a small click that allows you move it just a little when in the middle positions. If set up right you can get rid of a lot of the noise with proper cable tensioning, but you probably will not eliminate it.