Because it lost the war.
For all we know, the people(s) that inhabited South Africa when Europeans came could have genocided/expelled previous populations living there (who in turn could have genocided/expelled yet earlier populations), meaning that the land wasn't "theirs" in the first place. That's not even considering the ethics of claiming uninhabited land for yourself.
All to say that it is not necessarily as black and white as you present it, and that lots of evidence of 'crimes' may be missing because they happened during times where little or no history was recorded.
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