Hello, There are several ways to reproduce the problem that acolytes stop spawn in endless missions.
1: Complete Kuva Harvester (Kuva Survival Mission)
This will cancel the appearance of the Acolyte if the Kuva Harvester is completed between Acolyte communication and the time it spawn.
2: Complete Conduit Defense (Disruption Mission)
This will be cancelled if you successfully defend the conduit by defeating the Demolyst/Demolisher between the Acolyte communication and the time it spawn.
If this reproduction is successful, the Acolyte will not spawn