Why Did Holly's Mission Fail?

It has been a long time since I read this book. I recall two missions that Holly went on. One was when Holly goes back to the original warren where the rabbits were hiding underground. A construction crew gasses the holes. Another mission was when Holly goes to Efrafa warren to ask for does to mate with. The answer is no and Holly and the team are held captive. They eventually escape with the help of a train cutting their pursuers off. I hope this helps a little.