I have made my own save system, but I still use the save and load functions a lot for debugging. One of the projects I'm currently working on is an RPG, so I use it to save mid-cutscenes, or in the middle of a battle, or sometimes even before I reach a boss or start a battle. In all of these cases I have issues :
1. Mid-cutscenes -> I have tried using the timeline feature and just couldn't wrap my head around it, so I made a cutscene system where when a cutscene gets called, we stop player movement and enable a group with the cutscene name - in this group, we have a ton of waits, or stuff like waiting for a character to finish a walking tween so the next part gets called. This generally works, but sometimes it doesn't, and I believe it has to do with tweens.
2. Mid-Battle -> The battle menu that I have has hierarchies. When loading the save state, the hierarchies break, so the menu is broken, and shadows that were created when I spawned the battle sprites are also broken, etc.
3. I have NPCs that walk around using tweens. I decided on using tweens because the Tile Movement behavior doesn't account for the bounding box. In any case, sometimes I save the game before I test something, and when I load I get an error, making the savestate unuseable.
I absolutely agree that the save/load actions should not be used for actual save games and ideally we all should make our own save systems, but I think C3 shouldn't break when using it, and all default addons should work properly with it, or if it's impossible, it should be mentioned in the manual, so at least we can refer to it and workaround having to use it.
Edit : That being said I think these issues should be reported on the bug tracker instead of talking about them in a random forum post. At least I think that people who will run into bugs later can refer to this to understand why they keep getting errors on the devtool when trying to load a saved game.