MSF is a fantastic organization and a brave group of people, but they're doctors, not lawyers. People throw around the 'war crime' phrase without really understanding what it means.
Good article about the issue.
Usually the misconception is that a war crime is literally that - a crime (i.e., something that would be a crime in civil society) that occurs during war. So MSF's argument seems to be that this was the equivalent of manslaughter - "killing a human being without malice aforethought, or otherwise in circumstances not amounting to murder." But that's not what constitutes a war crime under the Geneva Conventions.
From the article -
"The mere fact that civilians are killed, that a hospital is damaged, doesn't automatically mean that there has been a war crime...It only becomes a war crime if it is shown that the target was intentionally attacked."