ISPC 3.1 lists both joomla 2.5 and joomla 3.6.4 but when you click 3.6.4 it loads .25 for installation. Is this an aps issue?
Please make a report in the bugtracker https://git.ispconfig.org/ispconfig/ispconfig3/issues so we can check that, maybe the aps installer mixes up packages when there are 2 packages for the same application.