Hi,
The WAG rate matrix in libpll is different from the WAG matrix that you can download here: https://www.ebi.ac.uk/goldman-srv/WAG/wag.dat
This is causing raxml-ng to fail some likelihood tests.
There are further details and discussion in my message to the testiphy list here: https://groups.google.com/d/msg/testiphy/wkpvzHVrnDs/L6FOB_HQAwAJ
-BenRI