Tough to diagnose without seeing what is going on.
For your awareness, the recommendation of the chain being in a certain gear (small/small) is simply reducing tension and creating enough slack where it is easier to remove and reinstall the wheel. Don't get hung up on that. All you should need to do is put the wheel on, get the chain in the gear it was in when you took it off and turn the pedals to make sure. If it's not in the exact gear, turning the pedals usually moves the chain so it corrects itself. Conversely you could take the wheel off in any gear, then shift until the derailleurs are in the small/small, then reinstall the wheel and put the chain on the small/small.
The rubbing on your front derailleur could be that you accidently shifted it and it is not positioned over the small ring, but it is on the large ring and you are trying to jam the chain on the small ring or vise versa.