I couldn't figure out a permanent fix for this so I just changed the Enduring Cry line in the combat routine to the following.
RegisterBuff("Enduring Cry", ret => !HasAura(LokiPoe.Me, "endurance_charge", MaxEnduranceCharges, 1) && LokiPoe.Me.HealthPercent > 95 && NumberOfMobsNear(LokiPoe.Me, 10, 3));
I made it so Enduring Cry will only go off if I'm above 95% health. Also there is an issue with the bot non-stop casting Enduring Cry if mobs are on the screen, but are not in LOS or not close enough to give you a charge. That is why I added the number of mobs near me section. That way EC only casts if I'm being swarmed, basically.
It's not perfect, but at least EC is usable this way. Feel free to make changes to the health percent (95), max mob distance from player (10), and number of mobs within that distance (3).