Rabbis have often used the forgery tack to wave away sources they found unacceptable. Spiegel discusses several such examples in his book Amudim beToldot haSefer haIvri, part II, pp. 252-275. His main topic is responsa which have been suspected as forged, but he mentions other books as well.
One well known example is R Yehuda heHassid's Bible commentary. It was published in 1975 by Y.S. Lange, who had already published many volumes of the Meiri's Beit haBehira and other manuscript works. Rav Moshe Feinstein was told that the commentary contains explanation which assume that passages in the Bible were inserted after the time of Moses. His response (Iggerot Mosher YD 3, 114 and 115) was that the book must be a forgery, or at least those passages, and that the printing must cease. Lange pointed out that these explanations were brought in the name of R Yehuda heHassid in a later book, Sefer HaZiyyuni - and R Feinstein's response was that the second book should be banned too.
Since then, it has emerged that this commentary is simply one more example of an ancient Jewish exegetical tradition which had no problem in seeing the Bible as a document which was edited over time. Read about it here if you want, or in the fourth section of the late Prof. Ta-Shma's book, Knesset Mehkarim, volume I: Ashkenaz, Jerusalem 2004.
I think this is an illuminating example that holds true for the some of the other cases Spiegel mentions as well (the Rema's responsum on Stam Yeinam, or the geonic sources requiring a menstruant to immerse herself in a "live" spring - see Dov Zlotnick's article in Atara laHayyim). The opinions may seem strange or beyond the pale today, but they authentic. You can reject them, but you can't erase them (you can try. I'll try to stop you).
On the other hand, there always have been genuine cases of forgery. But they tend not to present heretical opinions. Another example that Spiegel brings - Shaarei Teshuva. This collection of Geonic responsa, which has been discussed extensively in the past 15 years (see Neil Danzig, Tarbiz 58 ), contains many paragraphs which were either doctored or made of whole cloth. An example I once looked at: many sources condemn wine-songs because they lead to moral turpitude.
But in Shaarei Teshuva, it says this specifically against songs in foreign languages. Checking the manuscripts showed that those two words, "foreign language", are missing. Provisional conclusion - they were added later. But they never bothered anyone when the book was published, because everyone felt quite content with this anachronistic idea that Hebrew is intrinsically a better, more moral language.
Most medieval forgery seems innocuous to us. As far as I can remember, Moshe Botril was not writing heresy. The motive for forgery was self-promotion. The content was not usually insidious.
I am reminded of a book I once saw, and have no idea anymore what the title or the author was. But the author tells how, at some point in the 1930s, the Nazis unearthed the medieval Christian complaints against the Talmud - that it is full of anti-Christian venom, immorality, absurdities and superstition. The author took it upon himself to answer their charges, and his blanket solution was that the problematic passages had been planted by Christian censors. I can't imagine it had much of an impact at the time. But what really surprised me was that, living in Israel after the Holocaust, he still saw some need to publish this book. Apparently, he really believed the passages were forged. Today we know that all these passages existed long before any Christian had looked at the Talmud.
Even the slightly bizarre midrashim that Raymond Martini collated in Pugio Fidei and which did not seem to be found in any known collections of midrashim, were probably not invented by any Christian (Ta-Shma has some interesting comments on obscure midrashim that seem foreign, in his lecture on R Moshe haDarshan, Jerusalem 2001).
Those cases which do seem to sometimes fit the Haredi conception of forgery are modern - Besamim Rosh being the most famous example. But such examples are very rare.
The Middle Ages is often surprising to us. That's what makes it interesting - to see how, in some ways, we are strongly influenced by our predescessors, and in others, very different from them. Attempts to write out the dynamics of the past, but to retain its prestige, are infuriating to me.