Question Prefab instance problem. Missing Prefab Asset: source control question?

I get this error every now and again. And it usually messes up my games project and it destroys a lot of my scenes. Today in a project with about 30 scenes one of them just randomly got this error after I restarted unity. It was one of the most recent scene I created, but not one I have edited in a few days.

I'm not manually editing any meta files manually or anything like that.
I've read this might be a git issue. This is the .gitignore I'm using, I suspect it not perfect
https://github.com/github/gitignore/blob/main/Unity.gitignore

What folders and files in a unity project should I source control and what should I not, is it enough just to source control everything in the assets folder?
Is there an official .gitignore file?
How do I prevent this missing prefab error from happening randomly again, what's causing this to happen