"The dirtiest stain on Europe's conscience" appears to have been the slave trade. I initially thought it would be the Holocaust but I googled your quote and though I can't find much more info than you gave, it does seem clear the author was discussing slavery.
The French contribution to The Enlightenment (a period of reason in the history of mankind) is the idea of Fraternity, or "the equality of man" (according to the author), and this had been exported in the form of democracy (the French had their own, famous democratic revolution, but also had a famous role in other democracies, let's just say it was a French brand (see: Statue of Liberty), and this is logically in direct conflict (colliding) with their burgeoning involvement in the growing slave trade.
This is the quote I found:
"The British had at least been determined there would be no slavery in Australia. But what of the great enemies, the French? Their revolutionary version of the Enlightenment, the equality of man, was also spreading beyond Europe. But these ideas now collided with the dirtiest stain on Europe’s conscience."