I might be missing something since first time playing as Rome with your mod. It is wonderful by the way! On VH getting attacked all the time still have yet to see AI use upgraded units but they are aggressive.
Anyhow the issue I found.. in tech tree where it allows you to upgrade/recruit legionaries. It completed the research had one turn to upgrade.. next turn can't upgrade can not recruit and level 2 regular barracks unit options were cut in half. No legionaries to recruit nor Hastati or Rorarii.