Yes, it's happened a few times. Interestingly, almost always turns out they have some history of sexual assaults/abuse - so I must have a nose for it.
I have lots of examples in my personal life, but I once worked for a children's charity as a volunteer coordinator (I was in charge of recruiting, background checking, and managing volunteers who worked one-to-one with children and their families). We had a volunteer apply who instantly just gave me a wrong feeling. I never felt this way about any of our volunteers before. My gut just said no. I took it to my manager, who supported me and my instincts. We had to go through the process of interviewing the volunteer and doing his DBS checks and go through all the motions, and he came with reams of references from all the other organisations he volunteers with (children's sports teams, scouts, etc.). On paper, he looked good, but there just something not right that I couldn't put my finger on. He turned out to have several recent traffic violations - like for speeding or running a red light or something similar - not bad enough to have lost his license, but more than one so he had quite a few points.
Anyway, my manager was able to use the driving issue as a reason we couldn't accept him (the role did involve the potential for some driving with children in the car). It all kicked up and he reported me to the national office and there was a big faff with our PR people about trying to not make it blow up into something that he could go to the media about. They finally managed to deal with him and get him to go away.
6 months later, I was sitting at my desk reading the paper and having a coffee before I started work for the day (this was in the days when we still read the actual paper!), and there he was in the newspaper having been arrested and charged with grooming a child online and other child sex offences. I was right. My gut knew. I got a thank you, in fact, from our national office for speaking up and making such a fuss, even though they'd previously been a bit annoyed at having to deal with him and probably would have rather I just approved his application.
Trust your gut. It's telling you something. The Gift of Fear is worth a read.