An interesting category of works are ones which are themselves totally acceptable to cite by anyone, but which contain citations that are totally unacceptable to cite by many people with such hang ups.
One such case is Rabbi Nathan Marcus Adler's monumental commentary to the Targum Onkelos, the Nesinah La-ger (which was initially printed as part of a Mikraos Gedolos type Chumash in Vilna in 1886, under the name Toras Elohim -- that's right, with a heh). As you can see below, in his explanation on Deut. 15.2 he instructs the reader to see further what "the author of ha-Korem" writes:
Who was "the author of ha-Korem"? It was Herz Homberg, the commentator to Deuteronomy included in Mendelssohn's edition of the Pentateuch. I am not surprised that Adler refers the reader to Mendelssohn's Chumash, but it is somewhat interesting that he refers to "the author of ha-Korem." Herz Homberg wrote a commentary on the Bible by that name. A part of it was included in the 1846 Vienna edition of the Biur. See below:
As you can see, there is no comment on the verse in ha-Korem. Thus, Alder is not referring the reader to ha-Korem, but quite literally, to the words of the author of ha-Korem (that is, Homberg). He means his words in his commentary to the Biur:
What was so bad about Homberg per se?
His reputation, for one thing. Below is an abstract of an article about Herz Homberg:
The image of the educator and maskil Naftali Herz Homberg (1749-1841) is almost universally negative in Jewish historiography. He is generally described as a radical enlightener at best and as a corrupt opportunist at worst. In the words of one historian, "he hated Judaism with the utmost hatred." This negative depiction is primarily the result of his activities in Galicia as the supervisor for the German-Jewish schools on behalf of the Austrian government The present article demonstrates that this negative image was first created in the 1860s with the partial publication of archival documents by the Viennese historian, Gershon Wolf. These documents, as interpreted by Wolf, are practically the only source for Homberg's sullied reputation. The view of Homberg that is offered here differs sharply from the way he is usually portrayed in Jewish historiography. This is achieved through a brief examination of several of Homberg's works, a description of the Austrian historical context, both Jewish and non-Jewish, a critical look at Wolf's publications, and the presentation of newly-discovered archival material. Homberg was, in fact, an enlightener in the mould of the Josephinian enlightenment. This enlightenment was fundamentally religious, yet believed in the supremacy of the state over the church in non-ritual matters, and in state-sponsored education that emphasized the formation of a religion-based moral character. Homberg, who saw himself as a student of Mendelssohn, was never alienated from Judaism, nor did he ever call for the abolition or weakening of the ceremonial law. There is no evidence that he himself did not observe the commandments. He did, however, support the full integration of the Jews in the Austrian state, and the consequences of this integration.
Despite the contention of the article that Homberg's ill reputation is derived from a historian's interpretation beginning in 1860 (and is really undeserved), the fact remains that he was quite despised by traditional Galician Jewry, and his reputation as one who "hate[s] Judaism with the utmost hatred" preceded 1860 and derived from the man and his life. As an example, it was decreed in 1812 that any Jew in Galicia who wished to be married had to be quizzed in German on Herz Homberg's Bene Zion, which I assume probably helped the book's sales; don't think this went totally unenforced either. Just try to imagine all those young, early 19th century Galicianer couples trying to make heads or tails out of the book below.
Furthermore, R. Adler was not "soft" on Reform, and was living on the Continent, and not England, during Homberg's heydey. He knew exactly who he was. However, one supposes that R. Adler did not have hang ups about citing questionable characters. But certainly many an admirer of the Nesinah Le-ger commentary would not wish to follow his advice and see what Herz Homberg had to say on the subject or would not wish others to do so!
Interestingly, below is something I noticed recently, although I can't say if it was an intentional distortion, a Freudian slip or only a mistake. In Aryeh Newman's Studies in Bereshit, his 1973 translation of Nehama Liebowitz's Torah studies, the following appeared in the bibliography of sources:
As you can see, somehow only four of the five Biur commentators are mentioned. The fifth, Herz Homberg, is not mentioned at all. In point of fact, Aaron Jaroslav, who commented on Numbers in the Biur, is an almost totally obscure figure. Most people aren't even aware that he was a part of it, and very little is known about the man. The same cannot be said for the other four, Homberg included, all of whom were famous or infamous in their own way. Thus, it seems strange that Herz Homberg was left out as an oversight, but it is still possible.