Bad Pathfinding:

• Allies: aren't getting stuck anywhere near as often at my base compared to what they were doing near launch. I haven't noticed it recently, but they likely still get stuck depending on how complicated your base gets. Beyond that, any pathfinding is fairly basic, they're not smart about it.
• Enemies: I've seen them navigate through trees and up simple mountain trails when they're running away from me. And if you attack them, and hide up on a nearby cliffside they usually just get stuck at the cliffside below you trying to walk into the wall.

Dumb/Static enemy behaviour:
Yeah this is still very basic. They usually stay in the same place unless they are running away, chasing you, switching targets, or using an ability that forces them to move. It's trivial to just hide behind a tree or a boulder and attack them until their health is low enough to catch. They won't actively try to adjust their angle of attack to compensate for objects between you and them.

Character clipping issues:
The only player structure I still have clipping issues with is one structure meant for increasing your storage/showing off pals at your base. Even then I only saw one player get stuck in it once recently. But he was probably jumping around on top of it for that to happen. It's rare to see issues at the level we saw at launch.

Really weird physics issues:
The one I can remember off the top of my head was where an attack could launch a character up into the stratosphere and then they would fall and instantly die when they finally hit the ground. I haven't seen anything like that in months.