What happens is that before sync starts, a lock file is created to tell other clients that sync is in progress, and once it’s finished the lock file is deleted.
It’s now part of the way sync works so this behaviour can’t be disabled unfortunately. I’m planning to write a post to explain why these changes are necessary as it’s true they can cause small annoyances like this.
Best if you can is indeed to exclude the joplin sync dir, or just the lock dir as that’s where files are created and deleted.