Blood does the same thing that it does when it senses a wound. It begins to clot. It causes inflammation. As a result, doctors must give patients anti-clotting medicine during the operation to thin the blood. This process creates a small percentage of risk to the patient.
Most injuries are temporary and self-limited, but some lead to a delayed recuperation.
The process also requires transfusions of blood. In general, the more transfusions, the more possibility of complications. What doctors would rather do is fool the blood into thinking it hasn't left the body. One biocompatible machine uses heparin. Heparin is an anti-clotting factor found in many tissues, such as the liver and lungs.