If you believe the reports in the Mainstream media, the Egyptian military woke up this morning and decided they needed to kill a few dozen members of the Muslim Brotherhood.  The Military had a press conference today in which they defended the shooting/gave their side of the story.
According to the military spokesman Ahmed Ali, a group of armed men attacked the army while others climbed on top of buildings and threw molotov cocktails.  “The situation was no longer peaceful.” Ali said.

Ali stated that one soldier is currently undergoing surgery for a
gunshot to the head, adding that both birdshot and live rounds were used
against the army.

He claimed that protesters were incited to
perform acts of violence against the armed forces, and that they were
warned several times against attacking or vandalizing any military
installations. Ali added that the army has been present on the
streets for 10 days, and that the only thing that could have changed the
situation was the actions of the protesters.

In response to
pictures of dead children that have been going viral, Ali stated that they
were pictures of children killed in Syria over a month ago.

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army kills enemies, not children. This is all a campaign against the
army, a form of psychological warfare,” he said, adding that this
“informational warfare” was intended to create sectarian strife.

An injured Egyptian soldier, Mohamad Ibraheem seemed to back up Ahmed Ali’s statement

said he and other soldiers were there to ensure the safety of the
people, but came under attack with gunfire, firebombs and bricks. He
said many of his colleagues were hit.

Police General Hany Abdellatif stated that what began as rock throwing
against the army, turned into gunshots at the army, leading to the death
of an army officer and conscript.

Abdellatif said: “[The army] Dealt with and controlled [the situation].”

interim President Adly Mansour was reported to have appointed a
judicial committee to investigate Monday’s shootings. A presidential
statement expressed “deep regret” for the violence, but went on to say
the shootings took place during an attempt to storm Republican Guard

There is no proof the military version is true, neither is there proof the Muslim Brotherhood is telling the truth.  The answer probably exists somewhere in the middle, but the mainstream media should be telling both sides.

Sources: Egypt Daily NewsGlobal Security