Your followers that use SimpleFollow plugin use QuestTools to upgrade the gems. Moreover, SimpleFollow ignores follower's QuestTools setting for minimum upgrade percentages, it reads it from leader's QuestTool setting. Even in a case when the leader upgrades the gems with Adventurer plugin.
Real solution would be to fix QuestTools to ignore the 50-maxed gems during an upgrade, similarly how the Adventurer does. Temporarily there are several ways to avoid it:
1. Move all 50-maxed gems down in the list of follower's QuestTool settings and put low percentages in leader's QuestTool setting. Note that eventually, when all the follower's gems get upgraded this method will end up at 50-max gems. Setting 1% on leader may prolong it for quite some time though.
2. Move all the 50-maxed gems down in the follower's QuestTool and move upgraded and unused follower's gems to an invetory of follower's alts. Without the gems your follower will drop new ones and start to level them again, giving you several hundreds of smooth Grift runs.
If you have any cool ways to avoid this problem, let me know guys. Been fighting it for 3 weeks now.