The goal in this case was to improve soybean amino acid content (soybean is a major world crop, with Brazil being one of the top suppliers). Pioneer- one of the major seed companies- created a transgenic (moving a whole gene from one organism to another) soybean with a gene from Brazil nuts. That gene turned out to be the one that produces the protein in Brazil nuts which causes an allergic reaction and the soybeans actually seem to cause a reaction in people who consume them (I'm glossing over a bunch of technical details in the paper).

It's not hard to image, with an existence proof like this, that there are many ways that GM crops could increase the risk to consumers.

Any biologist I've trained with who understands transgenics and immune response would immediately note that this was a fairly obvious potential risk/outcome provided the source gene's properties had been identified first.