It can be a problem, but I haven't run into it too often.
The most annoying one for me was that I started Rock Band with the controller so it would be easy to set up a new band, rather than using an instrument to do the input. I then turned in the guitar and proceeded to rock out for a few hours. Having been logged in to the controller on #1 rather than the guitar on #2, I didn't get any credit for achievements because I wasn't actually IN the band. My controller was just there with me logged in but not counting as a group member.
Doh!
I had to start a new band to get those first several achievements.