When I first heard "ontology recapitulate phylogeny" it was explicitly said that this means that the early embryos of vertebrate species are similar, that many features that are clearly the same in the embryos of different species will develop into adult structures that are homologous - i.e. the pharyngeal pouches developing into gills in fish but into the jaws of mammals.
This is true.
I did hear the claim that the embyo supposedly passes through the entire evolutionary history of the particular species, but it was always pointed out that this stronger statement is false. So when I hear that this is a controversey in the evolution/creation argument, I, for one, don't understand what the fuss is all about. The truth is, ontology
does recapitulate phylogeny, in the weaker but well-supported sense. I don't know of anyone who claims the stronger statement.