What are two aspects of U.S Imperialism that Twain disagrees with?
Twain's primary complaint about imperialism is that the "Blessings of Civilization" as exported to "The People Who Sit In Darkness" are being "adulterated," with the exported version being quite a different thing to the home version. Effectively, he is saying that people are lured in with "pie," which does not accurately reflect what will be imposed upon them. It is not, in his mind, Christian. People who are promised protection are instead offered "brutalities and inhumanities." According to Twain in his satirical essay, "To The Person Sitting In Darkness," this shames the colonial nations and represents a mockery of Christianity.
Secondarily to this misrepresentation, Twain also criticizes the specific circumstance in which the US annexed the Philippines. Twain feels that the approach the US took to Cuba was far more in keeping with American values than the approach taken in the Philippines. He imagines the Filipino reaction to this discrepancy:
There must be two Americas: one that sets the captive free, and one that takes a once-captive's new freedom away from him, and picks a quarrel with him with nothing to found it on; then kills him to get his land.
As Twain describes it, the US should have helped the Philippines destroy the occupying Spanish fleet, but should then have left the nation "in the hands of its proper and rightful owners." Instead, the US chose to simply replace the Spanish as overlords of the nation, abusing the trust of the Filipino people who had been fighting for their independence. Twain suggests that, because the US had helped Cuba in securing its own independence, the Filipino people could reasonably assume that the US would behave similarly in its case, which did not happen.
Twain most clearly and famously criticizes imperialism in his 1901 essay "To the Person Sitting in Darkness". He criticizes the imperialistic activities of several countries, including Germany and Great Britain in the satirical essay, but since the question refers to American imperialism, this answer will focus on his American critique.
First, he claims that American behavior in the Philippines, which William McKinley and Congress had decided to annex after American victory in the Spanish-American War "liberated" it from American control, was contrary to American principles. Rather than annexing the islands, Twain contends, the United States should have liberated them, warning foreign powers not to meddle with them. But the United States did not do this, because they were tempted to play the "game" of imperialism that characterized relations among European powers. The result was a brutal war in the Philippines, one which raged on even as Twain was writing.
Second, Twain basically argues that imperialism is motivated by greed, not any desire, stated by missionaries and imperialists, to bring the blessings og "civilization" to people "sitting in darkness". Twain mocks these pretensions of what he calls the "Blessings of Civilization Trust" (a reference to the large monopolies that dominated the American economy at the time), arguing that in the end, imperialism is about exploiting poor, colonial peoples for the profit of rich nations.