I can't find any good information for this issue on the GitHub except for one unreplied post.
https://github.com/magefree/mage/issues/5079AI will randomly, but almost always, enter a state where it takes upwards of 20s-3mins to resolve individual triggers on the stack, phase changes, or attack steps.
It's usually, but not always accompanied by an 'Ignoring messages out of order' in the client log, but seeing this message is a guaranteed death sentence for an AI game.
This, and
https://github.com/magefree/mage/issues/6738 are the two biggest reasons I can't even use the program for reliable deck testing at the moment.
Both issues have been progressively getting worse over the course of the last few updates.