Weird phylogenetic tree
Anyway the chances are this is gene duplication. It will be a housekeeping type gene or else histone that sort of thing. You simply map the different genes onto the various metazoan classes. In your case nematodes and arthropods are basal metazoan, so their is correct given the clade they form part of all all representatives is that gene.

There is nothing weird you just need to read the deep phylogeneticists work like Tom Caveliar-Smith and Sandy Balfour, possibly Blair-Hedges

There are alot of eukaryotes prior to the invertebrates, just look at the Cambrian explosion