Biggest red flag for me was one I pretty much was aware of before I went in.
I can't remember if it was through a third-party recruiter or direct to the company, but I was fairly desperate for a sysadmin job, and I might have been out on the streets already at that point. I strolled on down to see this place, which was nestled behind a Motel 6 and a future mental health clinic; charming neighborhood.
I met the HM and I swear to god that he was a dead ringer for an old boss I'd had years ago. Once I got over that shock, we had a little chat, and along the way of course, he said "you know that we're the biggest service provider to the pornography industry?" and I said "yeah" and he said "you don't have a problem with that?" "nah... [I NEED THIS JOB NOW]"
I didn't get the job of course, but I really dodged a bullet, and definitely did not need something like that in my past or on my résumé.