It's going to be hard to find a source properly outlining why the Church banned Les Miserables because oftentimes, few explanations are given for why the books in the Index Librorum Prohibitorum (List of Prohibited Books) end up there, but the Catholic Church generally puts books on the Index on bases of anti-clericalism, heresy and blasphemy. However, we can find out some reasonable factors to answer your question if we consider the general moral outlook of the Church, and the context surrounding Victor Hugo and the book in that time period.

Victor Hugo in the novel gleaned over controversial issues on politics and religion, especially anti-monarchism. Les Miserables features the June Rebellion, an anti-monarchist insurrection in Paris at that time, and contemporary critics criticized that Victor Hugo wrote in a sympathetic tone with the rebels. Not that the Catholic Church necessarily likes monarchies and hates republics, but the political situation in France was different. France at Victor Hugo's time was in a period of turmoil with several conflict between monarchist and republican factions, and in France republicanism was associated with anti-monarchism, and monarchism associated with support of the Catholic Church since the two were long associated w/ each other. So, there was that, French republicanism in the mid-19th century puts you in trouble with the Church.

Second, Victor Hugo was an ardent anti-Catholic and anti-clericalist even though born and raised Catholic, and noted the constant Catholic attacks on his work, so there also was that.

Though many people will point to you that the story in Les Miserables was perfectly compatible with Catholic and Christian teaching, that's not my point and beyond my scope as again, I am not an expert in literature, but the political situation in France and Europe at the mid-19th century at the time Hugo wrote the novel, and the author's outlook meant that the Church was suspicious of the novel. FYI, the Church also put his other novel, The Hunchback of Notre Dame in the Index Librorum Prohibitorum.

If you are finding a more detailed analysis, such as analyzing the themes of the plot, I'll not do that since I'm not an expert in literature or in Les Miserable to analyze what in its content made the Church ban the book.