So... since no one has answered this question yet, I'm gonna give it a shot. This is my first attempt as an active redditor (and a non-english speaking one too) so I apologize in advance for all the mistakes (grammar included). I don't really have any English language sources because most of the material I've studied is italian/french/german.

Premise: When talking about the Catholic Church we have to make clear that, even though it's a well organized and extremely centralized institution, we're talking about a huge human organization spreading over lots of different countries and through all levels of society. There's an official theological-doctrinal standpoint expressed and carried on by the Pope, but you also have to consider the different interpretations and point of views of every specific school of thought, scholar, congregation, theologian, bishop, catholic societies and parties, priests, followers etc. That said, the general opinion mostly reflects or it's highly influenced by the Pope, especially in a context where the freedom of conscience (remember the Index Librorum Prohibitorum was only formally abolished in 1966!) was not accepted as part of the values of the Christian society, so the debate is never totally open inside the catholic community.

Context: During the age of scientific racism the Catholic Church was coming through a very difficult approach with “modernity” and the rising of new political and philosophical ideologies (nationalism, socialism, rationalism, positivism...) that exploded during the Enlightenment and spread all over Europe after the French Revolution, which was itself a huge shock for the Catholics and the Holy See. The first approach with the modernity during the 19th century was to condemn every idea and concept considered to be unorthodox, heretic, or in contrast with the catholic doctrine, in order to protect the Christian faith from the ongoing secularization process of society. The most solemn and explicit reaction to the modern ideologies was the Syllabus of Errors, a document issued on December 8th 1964 as part of the encyclical Quanta cura by Pope Pius IX, which can be seen as a collection of all the counter-revolutionary typical themes of the late European romanticism (De Maistre, Lamennais, Donoso Cortes, Taparelli d'Azeglio among others). In this context Leo XIII (1878-1903), Pius IX successor, started to face modernity from a different point of view, influenced especially by the neo-scholasticism and a more political attitude aimed to confront and challenge the liberal culture and the modern sciences, with the aim to recreate the greatness of Christianity, as it was before the Revolution. In his new ideology of Christianity, the Catholics must deal with the modern national States and their laws, shaping the society, politics, the mass culture and the economy (catholic social teaching). This new approach also affected the way the Church managed and promoted the new missionary boost in the late 19th century, because the expansion of Christianity both within the modern European society and outside the European continent were part of the same plan of bringing back the power of the Roman Catholic Church over the secular States. Spreading Christianity became in the age of Imperialism and Colonialism very much connected with the idea of spreading the Civilization, because the only true civilization in the mind of the catholic thinkers in Europe was the Roman Catholic civilization. In this mentality, there was no doubt that the savages had to be converted to the true religion and at the same time educated to the highest level of European civilization for a man of the 19th century.

So did the Church have an ethnic/racial prejudice? The catholic theology rejected and condemned, even though not officially, the Darwin evolutionist theories (which at the time was called “transformism”) and every scientific justification to the biological difference of human races in contrast with the Holy Scriptures and the doctrine of monogenism (as opposed to the predominant polygenist theories), which was considered as the fundamental and irrefutable interpretation of the the Book of Genesis. If we all come from the same parents (Adam and Eve) then we all deserve a chance for salvation. Moreover, the official theology and the catholic philosophers refused the naturalistic approach for the study of the human being, because the man had to be seen as a combination of divine and natural properties, as the most important creation of God and not just an animal among other animals. While polygenists generally saw the white (or “caucasian”) man as the most perfect evolution of the human being, all other less evolved human races were seen as the link between human perfection and animality, catholic scholars and theologians wouldn't accept the idea of the direct natural evolution from animal to human without any divine intervention and refused the idea of different human races and levels of evolution, always focusing on the common original background of languages and religions (this kind of approach influenced scholars like Wilhelm Schmidt and his theory of Urmonotheismus). A much popular justification (not only among Catholics) for the physical and cultural differences between human groups, in particular for the existence of Africans, was the old medieval theory of the biblical curse of Ham's son Canaan, because the idea of a divine damnation seemed to explain the eternal condition of slavery and savageness and suffering in the African continent. This theory was often mixed with the old belief that racial and cultural differences among men had a lot to do with climate conditions and geography (Montesquieu) and lead to the concept of degeneration from an ideal human to a savage or less civil kind of human. While all scientific racist theories are based on the deterministic idea that some races are less fit than others, and so they are condemned to extinction or eternal slavery, the catholic weltanschauung was based on universalism and the belief of perfection of the divine creation. The idea that all physical and cultural differences between men are just accidental, depending on the environment. That means every man in the world could embrace the words of Christ, whose message was for everyone including the savages. So, indeed there was a prejudice towards non-european, non-catholics, non-civilized humans, but none of these conditions were considered to be eternal or definitive. This was also the main catholic justification for colonialism.

The approach towards savages in the late 19th century didn't really change much from a theological point of view, since the age of Francisco de Vitoria and Bartolomé de las Casas in the 16th century. The savages were considered at a lower level of humanity and civilization, so the European conquerors had the right (but also the duty) to expand the word of Jesus Christ in the name of the Roman Catholic Church, and of course they could do so even against the savages will. What really changed in the age of Imperialism, especially after the Berlin Conference of 1884-85, was the attitude of missionaries (which ultimately lead to the birth of a new discipline called missiology in the early 20th century) who understood that if they wanted to convert more people and in a more efficient way, they had to learn the cultures, languages and costumes of the savages they wanted to convert and civilize. They also realized that colonialism could have been a great advantage for the expansion of the civilization in Africa and eastern Asia. However, the missionaries often reflected the mindset and political views of their mother country, rather than the universal catholic church mission. So in this hyper nationalistic world, the competition between colonial powers and missionary congregations of different countries were high and didn't always bring consistent results in terms of evangelization and civilization. Missions and colonialism have been pretty much connected in practice until pope Benedict XV apostolic letter “Maximum Illud” (1919) formalized the role of missionaries, their relationship with indigenous cultures and the colonial governments. The biggest improvement in this process of emancipation from the colonial system was the increased attention on the creation and formation of local indigenous clergy and the explicit rejection of any nationalistic interest in the evangelical mission.

So we have to understand that there are two different levels of acknowledgement in the evangelization/colonialism process; one level is the theology, the ideology of civilization and another level is the practice of converting and expanding the civilization “on the field” which connected the missionaries with the secular policymakers in the colonization process: the latter understood that religion was fundamental to justify the expansion of civilization, and the former knew that they couldn't really do much without the help of the homeland governments.