That message is probably from ffmpeg failing before it even starts encoding. Since you are using CPU transcoding, it is either a permissions issue with the output directory or the disk is full or something.
Jellyfin 10.10.3 (Docker)
Ubuntu 24.04 LTS
Intel i3 12100
Intel Arc A380
OS drive - SK Hynix P41 1TB
Storage
3x WD Red Pro 6TB CMR in RAIDZ1 (JF Library)
then i think it is a permission issue because i add another media after this one and i have no issues with that one, Is it possible that the problem is with the mkv file itself?