Either the bottom/tip of the derailleur, where the chain sits on the smallest gear, hits on the chain
Is the chain on the small rear sprocket when this happens ?
every gear configuration would work without rubbing
There's no need to use every gear, some gears aren't meant to be used, some gear ratios are possibly the same and some would be so close in ratio that you wouldn't notice the difference.
Don't cross chain and you probably won't have a problem.