Fratricides or just deaths in general?
Casualties post-war (covering all of the four major surrender dates) was probably just part of the cost of doing business.
With only telegraphs as a means of modern communication, trying to get the word out to everyone that the time for sanctioned killing was over would have been nearly impossible.
The lawlessness in the south (beyond the range of the Provosts' muskets) started during the winter of 1864 (thanks to bushwackers) and continued until Federal troops rolled in and instituted martial law.