Because they didn't get the command.

War crimes are typically committed by special units, selected/trained specially for this task. Ordinary marine is not ordered to do such things in "normal" circumstances. Its most important reasons:

• The military won't demoralize the soldiers with it. Not because they would be nice guys, but because the morale of the soldiers is very important to win the war.
• Very serious war crimes can be done by quite a few people if they are organized "correctly", there is no need for regular soldiers for that.
• War crimes are being done typically in secrecy, because they would be a PR disaster in the case of reveal.

The result is that serving as a soldier in an army commiting war crimes¹, it means most likely that you are sent to fight, and maybe you die. And most likely you won't ever hear from any nasty (except the ones committed by the enemy), only after the war - and only if you are on the losing side. If you are on the winners', then the "history is written by the winners" rule is applied.

¹ If there is a total war, then the "commit or not to commit war crime X" is a non-issue. Only the result of the war is an issue.

They didnt refuse to kill civilians because:

1. It is a soldiers job to follow orders.
2. It would of been very hard to distinguish between civilians and partisans.
3. WW2 was a war about living space for germans & due to that they would of had to go eventually.
4. Once the men of a peasant family are gone the remaining members could not feed themselves & were therefore a burden to the country.
5. It was all part of nazi ideology.

Many soldiers refused and got away with it.

Especially if they did not question the murders in principle and merely said that they were "too weak" to participate themselves.

Others obeyed because they did not think they'd get away with it.

A policy of public punishments for refusals might have been one way to ensure compliance, but it would also have highlighted that those refusals did happen rather often. It was in the interest of the Nazi leadership to sweep these incidents under the rug, figuratively speaking.

Others obeyed because they agreed with the orders.

(Here is the German wikipedia entry on refusal of orders.)

So to answer the last question: Mostly, the generals put those who would not shoot unarmed children into places where they could shoot armed enemy soldiers instead (and be shot at by the enemy in return).

TL;DR The Milgram experiment has shown that people follow authority figures.

I think you'll find the Milgram experiment to be of interest.

The aim of the experiment was to test obedience to authority experiments, specifically with the aim of answering questions regarding why Axis soldiers committed atrocities.

The procedure of the experiment was for the test subject to administer (fake) electric shocks to a person who was answering questions. They got a shock if they answered incorrectly. The experiment found consistent results that men from many different backgrounds would 'shock' the learner when prompted by the authority figure.

Milgram summarised his research in this way:

Ordinary people, simply doing their jobs, and without any particular hostility on their part, can become agents in a terrible destructive process. Moreover, even when the destructive effects of their work become patently clear, and they are asked to carry out actions incompatible with fundamental standards of morality, relatively few people have the resources needed to resist authority.

Concerning your questions, beyond the original "why didn't they refuse" one: the massacres definitely caused psychological problems for many soldiers, even the SS - to the point that Himmler himself decided to replace shootings with gas chambers and have prisoners and local auxillaries handle the victims and their bodies as much as possible. Summary from Wikipedia (paper sources there, bolded sections from me):

After a time, Himmler found that the killing methods used by the Einsatzgruppen were inefficient: they were costly, demoralising for the troops, and sometimes did not kill the victims quickly enough. Many of the troops found the massacres to be difficult if not impossible to perform. Some of the perpetrators suffered physical and mental health problems, and many turned to drink. As much as possible, the Einsatzgruppen leaders militarized the genocide. The historian Christian Ingrao notes an attempt was made to make the shootings a collective act without individual responsibility. Framing the shootings in this way was not psychologically sufficient for every perpetrator to feel absolved of guilt. Browning notes three categories of potential perpetrators: those who were eager to participate right from the start, those who participated in spite of moral qualms because they were ordered to do so, and a significant minority who refused to take part. A few men spontaneously became excessively brutal in their killing methods and their zeal for the task. Commander of Einsatzgruppe D, SS-Gruppenführer Otto Ohlendorf, particularly noted this propensity towards excess, and ordered that any man who was too eager to participate or too brutal should not perform any further executions.

During a visit to Minsk in August 1941, Himmler witnessed an Einsatzgruppen mass execution first-hand and concluded that shooting Jews was too stressful for his men. By November he made arrangements for any SS men suffering ill health from having participated in executions to be provided with rest and mental health care. He also decided a transition should be made to gassing the victims, especially the women and children, and ordered the recruitment of expendable native auxiliaries who could assist with the murders. Gas vans, which had been used previously to kill mental patients, began to see service by all four main Einsatzgruppen from 1942. However, the gas vans were not popular with the Einsatzkommandos, because removing the dead bodies from the van and burying them was a horrible ordeal. Prisoners or auxiliaries were often assigned to do this task so as to spare the SS men the trauma.