In this case my understanding is that the group was basically new to the particular topic and data analysis technique that they were studying. At some level th

In this case my understanding is that the group was basically new to the particular topic and data analysis technique that they were studying. At some level their errors were understandable, it would have been easy for anyone new to it to make similar errors. But when you start on a new topic as a researcher it's really incumbent on you to do your background reading and make sure you understand the field you're contributing to. In addition to that, Nature clearly did not assign reviewers who were knowledgeable about that topic. So I would say that the first situation you laid out most accurately described what happened here. Obviously there can always be some Dunning-Kruger effect going on and it's hard to know what you don't know, so I don't think there's any easy solution. The main things that help when you're entering a new field are: 1. Doing a lot of background reading. A lot. 2. Showing a preprint to others in the field for their feedback. Of course if you're sitting on what you believe to be big results, it's hard to do these things because they will slow you down.