No, they were surprised to find genetic sequences corresponding to gene products that regulate the early development of neural systems in vertebrates. These genetic sequences are found in humans, but only because humans are vertebrates themselves.
The gene sequences have nothing to do with the specifically human nervous system, nor with anything corresponding to specifically human nerve function.
For example, one of the vertebrate sequences found was Tumorhead. The Tumorhead sequence is generally studied by examining the genome of the model organism
Xenopus laevis, which is a species of sub-Saharan frog, to the point where the Tumorhead sequence is usually cited in papers as a specifically
Xenopus sequence. And, if you look at the full citations of genes that were identified in the paper, you'll see that the paper's authors do the same thing, labeling the Tumorhead gene sequence as a
Xenopus sequence.
Would you describe the sub-Saharan frog
Xenopus laevis as having a human nervous system or a human nerve function, randman?
And, in any case, while the Tumorhead sequence found in
Xenopus generally governs the differentiation of neural cells into specialized nervous system functions in a vertebrate organism during embryonic development, an overexpression of Tumorhead proteins can actually
suppress neural differentiation without affecting neural development as a whole (see
this study).
So, the presence of Tumorhead in the genome of
Acropora millepora does not in any way mean that the neural net of the coral should thus be complex and differentiated, as it is in a vertebrate's nervous system. And while I'm no expert on neural development, it makes sense to me that an organism with both a motile life stage (requiring a more complicated nervous system) and a sessile life stage (which doesn't require a complicated nervous system) would have genes which allow it to develop either a more complex or a less complex neural system as needed, during the various stages of the organism's development.