Misterie, I'm not sure... probably best to ask your doctor! Where are the fistulas located? I suppose it's possible the pap could effect them, depending on how the OB did the exam and where they are located.
It makes sense that paps on thinning or gentle skin could cause the skin to bleed a little (even for people without crohns). It's just the way it is that as we women age, and estrogen levels go down, the skin begins to thin, and I think become more sensitive. Now that said, paps ALWAYS irritate my skin (pain and all), and I'm in my 30s. I think I get some of that discharge too, but not a ton of blood. You should really get checked out because there are so many reasons why what happened could occur.
I am very interested in women's experiences with crohn's & gynecology, I've had a lot of unique situations that I attribute to crohn's. It is important to have an OB who has some understanding that crohn's CAN affect that part of your body, even in some cases, it can spread there as well.
This applies beyond OBGYN issues: Crohns can be a major factor in your healing process, e.g. skin healing from a pap, surgery, or any trauma minor or major, or pain you feel in any part of your body. Personally, I believe that boosting your body's overall immunity is probably the best defense.
Hope things become clear, and you find some more concrete answers soon!