Summary of problems with claim:

The study of how genes control the development of structures is changing rapidly. An important lesson scientists are learning is that developmental pathways are modular, and that it is possible to replace one module in a pathway without changing the end result. Putting the differences in developmental pathway into an evolutionary context clarifies how homologous adult structures could be produced by slightly different means.

Full discussion:

Explore Evolution claims:

other scientists simply dispute the neo-Darwinian explanation of homology. They contend that there are important facts about homologous structures that Common Descent cannot explain.

They point out that when two or more adult structures appear to be homologous, neo-Darwinism tells us that those structures should have been built by homologous developmental pathways and homologous genes.
…
Contrary to these predictions, biologists are learning that homologous structures can be produced by different genes and may follow different developmental pathways.

EE, p. 44

These observations would only create a problem for common ancestry if EE were correct to assert that "homologous … structures should have been built by homologous developmental pathways and homologous genes." Like so many other statements in EE, this assertion is wrong, and to understand the examples Explore Evolution gives, it is necessary to provide more of a background in developmental biology than the authors do. See the Primer subsection for more detail.

In brief:

• Redundancies in developmental pathways allow the removal of certain stages in development without preventing development of the final form;
• The self-sufficiency of genetic "tool kits" allows the same structure to originate at a different stage in development or from a different part of the organism.

These evo-devo findings do not undermine assessments of homology, it merely shows that the definition of homology offered in Explore Evolution is inadequate, an error which, once again, undermines their treatment of an important topic.

For more on this issue, see the entry at the Index of Creationist Claims.