Almost all religions have prohibitions against killing; almost all adherents ignore religious rules whenever they would require acting against their immediate self-interest.

Buddhists are no exception. Sad as it may be, such atrocities are not unprecedented and have accompanied Buddhism throughout its history; just as they have accompanied any other faith.

If you are interested, the book "Buddhist Warfare" collects a few interesting essays on the topic: https://www.amazon.com/dp/0195394844

Yes there are those who distort religion, but many religions have war ingrained in their identities, their foundations. Their gods, as described in the ancient texts, sanctioned and blessed war. The Abrahamic faiths are perfect examples of this.

Buddhism, from it's source, is different in that its first espouser categorically denounced violence against all living things, which makes any Buddhist warfare a shocking example of human ills. The Buddha even goes as far as to denounce just retribution.

> Buddhism has a fairly explicit prohibition against killing

It is easily worked around by dehumanization of your opponents. In buddhism such people might be considered icchantika for example which is basically someone who can never reach Nirvana and thus killing these "non-people" is akin to exterminating pests.

Obviously, there are many ways to dehumanize someone and sadly this is happening in many societies around the world right now.