There's been plenty of discussion on this here before, and you might find the answer you want in the FAQ.

To summarize those posts, the book is filled with straight up wrong retellings of historical events. Diamond overstates the role of technology (and how different it was across the globe) and the degree to which the conquest of the Americas was a "done deal," often to the point of ignoring counter-examples to his claims.

I explain my own thoughts in this comment:

In a world where conquistadors bested Aztecs with with guns and Spanish friars set up missions in communities devastated by plague, Diamond’s arguments would matter. But this is a world where Tlaxcalans bested Aztecs, and Spanish friars set up many failed missions before gaining a foothold and witnessing the populations they disrupted fall to disease afterwards.

Thus, even if we validate with absolute certainty that the Eurasian continent gave its residents greater contact with domesticated animals, and that larger wild seed sizes were able to support larger urban populations, and that these in tandem gave Europeans a increased resistance to disease it wouldn't matter. History as Diamond describes it still would not have happened. It never did. The given effects did not happen, so we must question the validity of the causes.

As described in his introduction, Diamond wants to know why white people have all the "cargo." He pins that on the European conquest of the Americas, which was enabled by a certain set of factors. But the Americas were not conquered by guns, germs, or steel, and the difference in cargo has more to do with European decisions practices of exploitation post-contact than any paths of development pre-contact. Will resources and geography change the way a society operates? Duh. But Diamond shows real geography determining events that never happened and therefore could not have been the causes of current global inequality.

More can be written, but you might like to look at the 'Historians' views of Jared Diamond's "Guns, Germs, and Steel"' section of the FAQ, which discusses his arguments in depth, and one mentions an alternative to one part.

This is not to discourage discussion. More questions, data, and debate are welcome.

I would say that it is a combination of two factors. The first of which being the errors and indiscretions in the book itself. And the second being the popularity the book achieved, which has led to the propagation of some errors.

The book has good points, but given the gargantuan task Diamond set out for himself, he inevitably uses a broad brush. One of the largest errors the book makes, according to many academic reviews, is that it overemphasizes geography and climate as factors that shape the course of history, neglecting cultural features. From that perspective, it is accused of being determinist, that civilizations were "destined" to come to a certain end, which inherently neglects the autonomy of cultural groups. GG and S is also accused of being Eurocentric, not appropriately attributing the contributions of Arab and East Asian civilizations specifically, grouping their contributions to the more general "Eurasia", which is technically correct. But, because European civilizations are spoken of in much more depth and specificity, it is natural that a reader might think of Europe when hearing "Eurasia".

This isn't my area of experience, but he's also accused of misrepresenting the agricultural revolution.

Historians are used to badhistory by authors and the public, so if GGS was a small publication with a handful of readers, I doubt it would receive ire it does by the academic community. But, given the popularity of the book, the views it espouses are common among the public. Moreover, the book is written by a renowned academic with high credentials, lending credibility to the claims in the book. This emboldens readers to assert the thesis of GG&S as fact.

So I would argue that it is a combination of errors in the book, as well as the popularity the book has gained, popularizing those ideas.