I've looked through the source and I do not see any obvious additional logging that can be enabled to trace a single document through an ingest pipeline, sorry.
Although I'm not familiar with how Beats configures Elasticsearch, I had a quick look at the source and I see a single drop
processor here:
Is this the pipeline you're running? If so, it looks like it drops messages that do not have _temp_.message_type
set to TRAFFIC
or THREAT
and in the request above this field is SYSTEM
.