If both the upstream and your feature branch have made changes to Gemfile, you will likely receive merge conflicts on Gemfile.lock when you rebase your feature branch. Don't try to resolve these manually; you'll probably just screw it up. Instead do this:
git checkout --ours Gemfile.lock
bundle
git add Gemfile.lock
git rebase --continue
This ensures that you get a correct Gemfile.lock at each step along the way.