I think that you misunderstand what the article means by "evolved twice." Neurons certainly did not appear out of whole cloth in one generation, and the process involved many false starts and dead ends.
The question is, do all currently living creatures with neurons trace back to a common ancestor who also had neurons, or are there several neuron-having lineages alive today, each of which traces back to a different earliest-neuron-having ancestor. In the latter case, each of those neuron-having ancestors would have shared a common ancestor, but one that did not have neurons.
The lineage of all life on earth certainly creates a more complicated graph than a tree, but at the time scale needed to create a novel feature like neurons, it certainly looks like a tree. To say otherwise, you'd have to point to a case where genetic information passed laterally between species, rather than vertically from parent to child. This probably has happened [1], but is not so common as to make all tree-shaped charts misleading.
[1]http://en.wikipedia.org/wiki/Symbiogenesis