Even though Space Marines and Sisters of Battle fight along side as brothers and sisters against the enemies of the Imperium, there are times when they come into conflict. As the fighting arm of the Ordo Hereticus, Sisters sometimes need to be used against wayward Space Marines who have gone renegade, or simply have an interpretation of the imperial creed which is judged to be heretical. A good example of the first is the Soul Drinkers, and a good example of the second is the Space Wolves.
Now,in the tabletop game this could be done because troops were more comparible, but in the RPG this becomes tricky. Using the stats from Ascension for sisters (near the back) and comparing them to your average Marines, it appears that there is a huge imbalance. Sisters, though fine soldiers, would be shot to hell fighting Space Marines. Their armour is lighter, they do not have unnatural toughness, and they have really girly bolters compared to Astartes. In an exchange, a sister might be able to scratch a marine if she rolls high, and can only do serious harm though Righteous fury, while most Space Marine bolter hits will knock the poor girl to the floor. Add to the fact that there are far fewer Sisters than Marines (I reckon about 20,000 across the imperium but I could be wrong), and all of a sudden going after wayward marines is asking for a thrashing. How does this reconcile with the fluff?