I encountered a lot of bugs and issues. This list is long, but it's not as bad as it seems.
Things kept randomly getting deleted. I think there are a few causes of this. The Undo/Redo system is buggy. Sometimes things wouldn't undo. Sometimes multiple things would undo at the same time.
If you save your script with an error, there's a small chance the component will just get deleted from the Game Object.
Prefabs. You can't make modifications to prefabs in the scene. If you want two identical prefabs, except one value is different, you need two prefabs. You also can't see any of the prefab's Properties without collapsing it. I ended up not using prefabs for most things placed directly in the scene.
Can't rename assets.
You can't rename assets in s&box. If you rename your material or prefab, all references to it are lost. You also can't change the file location.
If I wanted to organize these food types into different folders, I would have to manually reassign every reference to them.
Filename issues Having spaces in file or folder names messed things up. This was confusing because it seemed to work at first. Also, s&box kept making file names completely lowercase.
The built-in pathfinding is very bad, especially when using a Hammer Map. Characters kept walking through walls and getting stuck.
I needed to constantly restart s&box.
Unity crashes a lot. S&box doesn't crash as much, but I needed to constantly restart it because it kept acting strange. Sometimes things would get partially hidden/deleted, sometimes my controls would stop working. This is to be expected with an early Work In Progress engine.
The asset browser is very slow. It takes so long to switch between the official Facepunch cloud assets, and your local assets in your project. You can favorite searches, but it didn't seem to work properly. This doesn't bother me too much normally, because I just open a bunch of asset browser windows.
This is worse in the level editor, Hammer. You can only have 1 window open at a time, and it locked my input any time I added a model to the level.
Multiple cameras active at the same time. They appear to work properly at first, but they don't really work that well.
Different behavior in Editor VS in Game. A few things behaved differently when testing in editor compared to when testing in the regular game play mode. It seemed to mostly be physics initialization issues.
Inconsistent Physics. There are many different types of physics with similar names, but they behave differently. Ragdolls behave differently from regular physics objects. When you drag a model into your scene, it's given a "Prop" component. You can click "Break into Separate components", but those separate components don't act the same as a Prop. Mainly, "IsStatic" on the Prop is different from "Static" on the Model Collider. I don't know if this is intentional. It's very strange.
Cloud Assets are scary. Most things on the "asset store" seemed to be stolen or improperly licensed. We only used Facepunch's stuff to be safe, but sometimes they would just become errors.
Hammer Editor. If you ask any level designer, they'll tell you Source2 Hammer is the best level design tool ever made.
However, it's terrible in s&box. It's degraded so much. I'm not sure if we're supposed to use it anymore. I wish Facepunch would either commit to updating it and improving it, or just delete it entirely.
One day we woke up to find broken screen space reflections forced on all our metallic materials. We couldn't figure out how to turn this off. Everything with a metalness texture has this. It's still in the game. We had to update all our materials to make it less obvious, but it's still on, lowering the FPS...
Inches. S&box uses Inches instead of Meters. We didn't realize and made all our models using meters. This didn't matter, but nothing lined up on the grid.