That usually happens when they engage battle with an enemy they won't attack (being of same religion). Currently, they are unable to engage with an enemy within the same religious group as you (being pagan, say Romuva, and attacking other pagans, Norse or Slavic for example). This was a side effect of a change with RoI, but we are aware of it. 
Using them against other religious groups (Christians, Muslims etc.) should still work though.
Using them against other religious groups (Christians, Muslims etc.) should still work though.