It's not that the logs are missing, it's that they're not getting included by your query.
The way journald associates log lines with process metadata is inherently racy.
This situation has improved some with the metadata caching changes, but IIRC there are still some holes where processes can log without journald associating accurate/up-to-date metadata with the logged info.
The lines would go missing mostly if the logs were collected two or three days later instead of immediately after the job finished (it was a job running for 24 hours), which leads me to think it had to do with journald expiring entries to save on disk space. A consistent log manager would expire them chronologically, but here the lines were missing from the middle or the end of the output, so not the oldest ones logged.
I had an automation recipe that would start a bunch of cloud instances, configure them and start certain job via a systemd service unit, and collect logs from this job 24 hours later. Initially, we were pulling these logs via journald as logs for that service unit. But then we noticed that random lines (1-5 lines out of maybe 40 for a single job) would be missing in about half the instances.
We ended up pulling those logs from files in /var/log instead, made courtesy of rsyslog. Not a single missed line.
Again journald is unreliable and as a whole should be nuked from the orbit.