I had a similar experience and actually came here and found the solution. I was trying to put a backup file from another app on my tablet, into NextCloud as a precaution. However, when I went to upload the file, the NextCloud app saw the folder structure of the internal storage, but none of the files. My NextCloud app had been given complete permissions for Photos and Videos, but that was not enough. Once I changed that to having storage scopes, and gave it permissions for the folder that the file was in, it saw them all. I know that GrapheneOS is more restrictive than stock Android, so it's possible the OS is creating a problem where stock Android would not have it. But the solution of changing the permissions to storage scopes, and selecting the folders you want, fixes this issue.