Roary_plots missing core genes?

[evanho550]

I'm new to bioinformatics, so please forgive if my question are simple or lack information. I used roary_plots on my newick tree file and core gene alignment, but one of the outputs is looking weird. My annotated genomes are from NCBI, aligned with Panaroo, and the newick tree is generated using raxml-ng. When I use roary_plots, I get three output files as expected, but the matrix seems to be missing the core genes for some reason. I suspect it's possible that the tree is overlapping the core genes, but wasn't sure how to verify if that was the case. Any suggestions or ideas are greatly appreciated.