Tab autocompletion looks to be affected too, at least on my system. Create a branch called 'complete_$(./foo)'. Then type 'git checkout comp<TAB>'. This gets autocompleted to

    git checkout complete_$(./foo)

If you hit Enter at this point without thinking you'll end up running './foo'. It should have expanded instead to something like

    git checkout 'complete_$(./foo)'

or

    git checkout complete_\$\(./foo\)