I just managed to solve my own issue. While searching for other users with similar problems i stumbled accross this post Unable to add music where they were also unable to download the logs zip because of their temp directory.
My exact issue was in my docker compose I mount the direction plex_temp like this
plex:
container_name: plex
image: binhex/arch-plex
network_mode: host
environment:
- PUID=1004
- PGID=1001
- UMASK=002
- TZ=Europe/London
- TRANS_DIR=/transcode
volumes:
- ./plex:/config
- ./plex_temp:/transcode
This plex_temp directory had the complete wrong permissions and was not owned by the plex user as it was meant to be. Changing the owner of the directory allows music to index and also solved my logs not downloading.