I like to ask what they like most about their work, which gives them a chance to talk about their job, the company, others in the company (usually), and their role.
Because that's not a warning sign at all! boggles
Most people of course answer this question in the same way an interviewee does when asked 'Why did you leave your last position?'. Nobody will ever answer 'that jerk across the hall, I can't STAND that guy'. They will answer something that gives some insight into the company culture. I don't think it's a coincidence, for instance, that easily half the people at Google I've put this question to have answered something along the lines of 'management chaos/confusion', 'the tendency for two internal projects to be competing with each other without even knowing about it', etc.
I should have added the followup to my first question is what they like most. Both can be very informative, of course, and following up with that helps put them at ease for the rest of the interview, since many interviewers aren't expecting a question like this one. But it's really worth it. An interview isn't just to answer 'will you hire me', it also must answer 'will I enjoy working here'. The second is much more important to me.
It's perfectly normal to have things about your job you don't like. What's so bad about talking about them?
What's all this fear about the boss knowing you have issues with the job? Everyone, repeat, everyone has some issue, however minor, with a job. Owners, managers, etc. already know this. It's not something to hide unless you're working in a really sucky place that can't handle any level of dissent. And in that case you should probably think seriously about leaving (unless you like that kind of thing).
Wanna know what my answer is to most candidates who ask me about something I don't like about my job? The bureaucracy. We are in a highly regulated industry and it can take an annoying amount of time and paperwork to complete some tasks and it gets tedious and frustrating at times. There, I said it. Believe me when I say that the people I work for are well aware of this problem.