Xeno Moral Stains
The mismanagement of the Earth's biosphere.
It turns out that the problems humanity had, dealing with climate changes and mass extinctions just before emergence are not especially unusual. The technologies that allow for emergence are typically built on older and dirtier techniques that are necessary intermediate steps and often cause dangerous pollution and ecosystem damage. Nevertheless, the Society Of Contemporary Races likes to see an acceptance of the seriousness of the problems and a properly organised and robust strategy to deal with them. It found Earth's response disappointing before and during the Dislocations and this definitely counts as a significant XMS. Fortunately, the establishment of the Resource Management World Government was viewed positively and has gone some way to mitigating moral disaproval with the state of Earth's ecosystem.
The Escaloda Extinctions
The first extinctions off Earth, for which humanity was undeniably and consciously responsible, were the trigger that turned concern into revulsion and resulted in the Limitation. The events on Escaloda are most likely, still the best known XMS of which humanity stands accused.
The New Cambrian Mirror Struggle
On the world of New Cambria the native ecosystem depends on a chemical model of life, which is superficially similar to the way it works on Earth but uses the opposite chirality for the native amino acids. Colonists from the Republic, by introducing Earth based species have provoked a deadly struggle with "mirror life" which, for whatever reason, (theories differ) the native species appear to be losing. Humanity was explicitly warned about this and its failure to acknowledge the problem or do much about it, is a big XMS.