There are some quirks with using Jellyfin+Kodi with external subs. It used to be solved by the "direct play" feature in Jellyfin4Kodi where it would just pass Kodi a link to the SMB/NFS shares, but the newest releases of Jellyfin have deprecated and hidden the server side feature that enabled that. I had a talk with the devs about it on GitHub and they don't really know if/when it's gonna come back.