Where Facts Go Missing: A Layerwise Taxonomy and Per-Layer Attribution of Information Omission in Air-Gapped LLMAgent Pipelines

Air-gapped and on-premises language-model agents can silently omit decision-critical facts at any boundary between source ingestion and final answer generation. We present a nine-layer taxonomy (L0-L8), an instrumented attribution harness, and a conditional omission waterfall that distinguishes deterministic software loss from behavioral non-retrieval. We analyze 75,476 controlled synthetic trials spanning five open-weight model configurations and two inference engines, together with a separate 372-trial real-agent pilot covering FHIR, PubMed, and SEC-EDGAR sources with LangChain and ADK orchestration. The weighted synthetic benchmark yields an omission rate of 0.574 (95% CI: 0.571-0.578); deliberately injected deterministic faults at L0-L3 account for 73.4% of weighted loss under the benchmark allocation. Increasing context length is most strongly associated with omission (odds ratio 7.43, 95% CI: 5.44-10.15). Completed server-profile analyses associate q4 KV cache and scaled RoPE with higher omission. In the real-agent pilot, 57.8% of traces are unsuccessful overall and 50.9% remain unsuccessful after excluding execution errors. These results establish pipeline-level attribution in a controlled stress test, but benchmark allocations, confounded model comparisons, and heuristic behavioral labels do not measure production prevalence or causal architectural effects.