The flap of skin left by the surgeon would be pulled across and sewed close, leaving a drainage hole. These were infections arising from the septic state of Civil War surgery. As you should have been able to see, the Civil War surgeon was interested not so much in cleanlieness, but speed. As such, and not knowing anything about antiseptic surgery, fevers arose. Of these, the most deadly was probably pyemia.
Pyemia means, litterally, pus in the blood.
It is a form of blood poisioning. A black spot, about the size of a dime or so, would appear on the wound. Before long, it would spread through, leaving the wound an evil smelling awful mess. The Hospital Gangrene of the Civil War is an extinct disease now.