You're not looking at any of the criticisms I've seen, then. Here's a brief summary, off the top of my head:
* Jared Diamond posits an explanation of megafauna extinction in North America that's heavily predicated on the Clovis-first hypothesis and the overextinction hypothesis. The former hypothesis is very thoroughly discredited, and the latter is also generally disfavored, especially in the it's-the-primary-cause way that Jared Diamond uses it. (Specifically, it should be noted that the megafauna extinction in North America also coincides pretty closely with the Younger Dryas, whose climatic effects were most pronounced in North America).
* The primary north-south/east-west transmission hypothesis doesn't actually hold that well up to evidence. The two things I'd note are a) local topography has a major effect on climate that's not accounted for, and b) if you look at the transmission of cereal crops, there's very little transmission between the Mediterranean/Mesopotamian basin and China basin but universal spread of maize along the vertical axis of the Americas--the complete opposite of what the theory predicts.
* I don't have a link handy, but I've seen someone more versed in the history of infectious diseases point out that the killer diseases that Diamond identifies don't appear to have actually become epidemic in the manner that Diamond asserts.
* Diamond also places way too heavy on emphasis on the unreliable accounts of the conquistadors in explaining how the Spanish conquests happened.
In short, the main problem with Guns, Germs, and Steel is that... it gets the facts wrong. And people have brought these complaints to Diamond previously, so it's not like he's aware that there are facts which destroy his thesis, and Diamond's response is to double-down on the thesis without trying to explain why the countervailing facts might be incorrect interpretations or whatnot, or providing other nuggets of insight to bolster his thesis, just continually reassert that he's right.
Try reading Charles Mann's 1491. It goes into more well-researched explanations of pre-Columbian cultures that would help you understand why Diamond's thesis is wrong.