Are you running your rails console in test environment or in development as it defaults to? Different database and environment configurations might be the reason for different behavior, also the note object might already exist in development db at the time you test it manually in console.
Either try running console in test environment:
$ rails c test
or better temporarily put debugger line inside your test code (you will need get 'debugger' gem installed if don't have it already):
it "should not destroy notification for like on comment" do
comment = FactoryGirl.create(:comment)
like = FactoryGirl.create_list(:like, 2, likable: comment)
debugger
like.first.destroy
note = comment.user.notifications.find_by(notifiable: comment, from_comment: false)
note.should_not be_nil
end