Sometimes I see this when a buffer is open to a file that has never been saved. This can happen when I start a new org file and try to do some agenda thing before I save it, or when some function/process opens an org-file in a new directory for example, and an agenda thing happens before it has been saved.
You could check to see if there is a
refile.org buffer open (not necessarily to the existing file, just one named
refile.org) but that has not been saved. I don't know why such a buffer would be open, but if it is, it might be a cause of that problem.