War is a nasty business, and I doubt you can find one where the hands of both sides are truly clean. I preface with this to point out that recognizing this simple fact doesn't invalidate larger, correct historical narratives, even though this is a common and unfortunate tactic seen by apologists for any number of deplorable causes. In this case, the answer of course is "Yes". Union troops did at times commit war crimes too, and I don't want to play atrocity Olympics with them about who did worse things, as they could be quite heinous on both sides, but I do want to stress that it neither removes culpability that can be ascribed to the Confederates for their own transgressions, nor somehow elevates or lowers the comparative moral forcefulness of the broader causes represented by the Confederacy and Union, respectively.

So, with that little preamble done, again, the answer is "Yes". The Confederacy is far better known for certain massacres of surrendering boys in blue, most famous being the Fort Pillow Massacre, where several hundred men, mostly black soldiers of the USCT, were gunned down in a racially motivated slaughter by troops under the command of Nathan B. Forrest. The racial angle is fairly important in context here, as neither side particularly disputes it as motivation, the Confederate apologists simply arguing that it was essentially excusable for that reason, playing into larger grand, racist narratives of southern fears about armed black men, which was the underlying driving force of much of the Confederate abuse of surrendering soldiers, restricted mostly to black soldiers for much of the war.

Published far and wide and becoming a battle cry of sorts, Ft. Pillow was especially galvanizing within the black community, as while not an isolated incident (Others such as Milliken's Bend, Poison Springs, the Crater simply never quite captured the public indignity), its publicity hammered home the point that they could often expect no quarter from whiter southerners, and despite Lincoln's initial promises that tick would be met with tack with regards to killing of prisoners, reprisal executions were not carried out. The result was many men of the USCT simply adopted the 'No Quarter" ethos that they knew to already be directed against them. Although this had the clearly positive impact of imparting upon them a sterner fighting spirit that even the Confederates acknowledged, it of course had a darker side too. One white officer of a USCT wrote that:

After Fort Pillow, my command virtually fought under the black flag. We soon found that all our men that were captured and all wounded that we had to leave were promptly killed, and from that [time] on my officers and men never reported capturing any prisoners, and no questions were asked.

When discussing what are essentially reciprocating atrocities, it can be a delicate line to walk, but context remains key here. Union killing of Confederates attempting to surrender, which occurred at the hands of both white and black troops, was known to be happening, and while at times, such as above, it was essentially allowed to continue without official censure, it also did not reflect official policy. This stands in stark contrast to the Confederacy, where if anything what crimes did occur were not even to the full extent that the Confederate government officially endorsed! In 1862, when the prospect of black troops cropped up, they were explicitly to be denied status as lawful combatants, and the Secretary of War himself endorsed killing them, or selling them back into slavery. The Congress went even further in passing a resolution the next spring that found white Union officers in command of black troops to be "inciting servile insurrection" and liable for execution if captured, although this seems to have been actually carried out in only a handful of cases at best, with the majority of those officers captured surviving their ordeal.

This turns us to the Union policy. There was no similar, broad edict that mandated the execution of captured Confederate soldiers, and in fact the Lieber Code of the Union offered explicit protections to them and is seen as an important step in the development of the Laws of War. The closest example was Lincoln's threat that, in the face of Confederate policy towards prisoners from the USCT, retaliatory executions would be carried out on a like number of Confederate prisoners. It was in many ways an empty threat, and in the face of Fort Pillow especially, Lincoln's failure to follow through was galling to the black community, where Frederick Douglass compared Lincoln's attitude as no different than *"the slaughter of beeves for the use in *the Army."

But it wasn't entirely without impact, and although small comfort to the men struck down in the fields or craters, it almost certainly did play a large part in nullifying the proclamation for the execution of white officers. It also at least helped in curtailing broader massacres of black prisoners than otherwise would have happened, as many Confederate officers, mindful of the threat, attempted to prevent abuse of those under their care. How effective we can see it as being however is conjecture, as at least in part it only helped to instill more of the "Give No Quarter" attitude so while ensuring that those taken prisoner might have a better chance of survival, it possibly just encouraged fewer prisoners to be taken in the first place as it allowed for easier plausible deniability, such as seen in the letter written by Kirby Smith to Dick Taylor in the wake of Milliken's Bend:

I have been unofficially informed that some of your troops have captured negroes in arms. I hope this may not be so, and that your subordinates who may have been in command of capturing parties may have recognized the propriety of giving no quarter to armed negroes and their officers. In this way we may be relieved from a disagreeable dilemma.

The dilemma of course being here having to treat these men as prisoners of war, or else risk Union retaliation. This group of captured troops were the exception at Milliken's Bend, where reports from witnesses attested to bayoneting of the wounded, such as one body later described as having "six bayonet thrusts after having fallen by a shot".

This underlying racial conflict was the driving force of much of the killings against prisoners carried out by both sides. The Southerners adopting a policy of "No Quarter" against what they saw as no different than rebelling slaves, to be treated without mercy, and the Union troops, most especially those black men so targeted, responding in kind when they knew they would receive no better. This was the "norm", insofar as we can say there was one, but there were isolated incidents beyond it. One of the more infamous examples of Union soldiers killing prisoners occurred in the fall of 1862, at Palmyra, Missouri, a state which perhaps more than any other was emblematic of a disregard for the niceties of war, with paramilitary groups on both sides - Union Jayhawkers and Confederate Bushwackers - often operating with little control by the military authorities they nominally obeyed.

Often not granted status as proper soldiers, and thus not protected by the Lieber Code it was understood that they could be shot out out hand, as happened on a number of occasions. The identification of these guerrillas with common criminals was not always far from the truth, and the distinction could be blurred considerably, with many bands as likely to prey on civilians as they were to harass the nominal enemy forces. Not that it soiled them too much in the eyes of the proper Confederate forces, and the non-military treatment, including executions, evoked much consternation with Confederate commanders. In a communique to his opponent Samuel R. Curtis, the Confederate commander Theophilus H. Holmes protested the "barbarity" of executions, but even then couldn't help but bring race into the picture, writing only two weeks after the Preliminary Emancipation Proclamation heralded the coming of armed, black soldiers, and warning that retaliation against them would be in the air:

The proclamation of your President apparently contemplates, and the act of your officers in putting arms in the hands of slaves seems to provide for, even that extremity. It cannot in such a situation be expected that we will remain passive, quietly acquiescing in a war of extermination against us, without waging a similar war in return.

Holmes' threat did nothing to stop what would happen a week later at Palmyra, where ten prisoners, both Confederate soldiers and civilians sympathetic as such, were executed, although Curtis claimed to have been unaware in any case.. Suspected of being involved in partisan activity, they nevertheless had no known connection with the disappearance of a local Union supporter, believed murdered by men under Col. Joseph Porter, for which they were killed in retaliation after ten days had elapsed following an edict by Union Gen. John McNeil ordering the return of Andrew Alsman.