The md files don’t show in the File Manager
I’ve seen this before and could not reproduce on demand, but the fix that worked for me was to open the file in a different editor (VSCode), save the file, then restart Obsidian.
Yes, please open a bug report. But first: the Controllers folder isn’t unfolded in Obsidian. I imagine you just forgot to do that for your screenshot, but it would certainly prevent the notes from showing.