I've only ran a few side missions but so far, the A.I. teammates are doing ok, enemies killed by them while in stealth still yell out which shouldn't happen. On the side missions I've ran,
1) the enemy NPC's voice overs when they're complaining seem to be on repeat with very little time between them speaking and sometimes they talk over each other.
2) sometimes when crawling, nomad's legs will go up in the air or he'll start crawling up in the air.
3) on the objectives board there are certain missions that keep saying there's new Intel even though everything has been checked and completed.
4) after taking out a convoy and collecting its contents, after using a designated vehicle for a mission and sometimes long after drones are completely out of sight, the option to focus on it stays on the screen.