I have also been experiencing most of these bugs! I have a few things to add:
1) When the terrain tool stops working, it actually acts as if the button isn't working. I play with an xbox controller, and the "x" button is what takes the terrain tool out/puts it away. I've noticed when the terrain tool starts to bug, I can't use the x button to "quick-add" things to my backpack either. Sometimes dying fixes the glitch, other times I have to leave the game and come back in.
2) We have noticed the beacons glitching almost to the point that they are useless. They "fall off" of vehicles and backpacks and can be seen hovering in random places. It then becomes hard to distinguish the beacons marking things vs the ones that randomly fell off.
3) The biggest bug I have encountered since the automation update is sometimes when I die and respawn, the ground is invisible. I can see completely through a planet. I play both on xbox and steam, and this has only seemed to happen on xbox. It can be fixed by "digging" in the invisible area which causes the segment of ground to appear.