The conflicts are happening in my notes files. That is to say: whatever note I happen to be editing that day. Every day there’s a new journal note. That’s what I used in my cli example above.
I don’t have issues with any of Obsidian’s system files. My basic ignore patterns are working fine for that.
It’s certainly possible that another Obsidian instance could be running, particularly on Android where it’s not clear whether an app is running or not. But Obsidian would also need to have the same note open for it to be the cause of the conflict and that is definitely not the case in several of the conflicts that have happened recently.
The main reason I mention Obsidian is that it saves more or less instantly such that it’s reasonably to expect the file currently being edited to be saved more than once per second. Lots of saves seems to mean more opportunities for conflicts.