From Michael Fellman, The Making of Robert E. Lee (2000):

Confederate hatred for black troops spilled over most lethally on the issue of treatment of prisoners of war. In several instances, Confederate troops shot down black troops rather than accept their surrender. In the two most fully recorded cases—at Poison Springs, Arkansas, and Fort Pillow, Tennessee—several hundred blacks were slaughtered after throwing down their arms; many instances of killing of smaller groups and of black retaliation went unrecorded in official reports.

As for Lee's army, recent scholarship has described the massacre of black troops attempting to surrender at the battle of the Crater, on the Petersburg front on July 30, 1864, in which many Confederate soldiers participated. As North Carolina major Matthew Love described the scene in a letter to his mother, his regiment refused to take prisoners and 'such slaughter I have not witnessed upon any battlefield anywhere. Their men were principally negroes and we shot them down until we got near enough and then run them through with the bayonet. … We was not very particular whether we captured or killed them, the only thing we did not like to be pestered burying the heathens.' If General Lee knew of this significant incident, he did not respond to it.

(Extract lifted from here.)