This reminds me of one case where a person published a phylogeny, a reader felt that it was flawed, and so they went over the code together. They discovered a

This reminds me of one case where a person published a phylogeny, a reader felt that it was flawed, and so they went over the code together. They discovered a major bug which, when fixed, completely invalidated the results. The paper was retracted. (I can't source this, because it was a conversation I had with a postdoc and I don't remember the details) In general, though, the fact that code isn't reviewed isn't the biggest problem with peer review. The problem is that it's simply very difficult to come up with the real problems if you're just reading a paper, even if they're lab experiments- just like you can't see the code, you can't watch them perform the experiments. With my own work, reviewers never actually pick up on what are the actual problems with the research (which I know only too well.)