In Crohn's disease, the inflammation goes through all the layers of the intestine and also can inflame any organ or structure that part of the intestine is next to or touching.
If you have a bad spot inside your intestine (caused by the CD), maybe starting with an ulcer, or perhaps a fissure, it can start a hole which eats through all the inflamed layers and into the next structure/organ. Sometimes it ends internally because there are no structures close enough or the structures around it aren't inflamed enough to burrow through, and it creates an abscess, which is just a little pocket of debris and infection. In time this abscess can cause inflammation also, and sometimes break through to another structure. Remember, skin is also an organ.
They can get complicated, branch out in different directions. I had a fissure from my anastamosis that created an abscess and fistulized throughout my peritoneal fat layer. They had to remove part of my peritoneum and graft another membrane to get blood flow to that part of my abdomen. At one time, this fistula had broken through to the skin surface, but it "healed" with remicade and 6MP. We didn't know I still had things brewing underneath, nothing showed up on any of the tests.
This is a very simplified explanation for a complicated physiological breakdown because of the CD, but I hope it helps you understand a little better.