Grounded language-model pipelines can be divided into three stages: selecting an object, retrieving passages for it, and using that evidence to answer. If the selected object must reach the reader, losing it breaks the handoff. Benchmark recall checks the dataset-linked object, which can differ. We audit 600 HybridQA questions across three selector families. On 1,463 resolvable records where the selected object matches the dataset-traced passage, exact key lookup and exact title matching return the object every time. With every ranked rule given the same decoded selected title, body-only BM25 omits it on 389 records (26.6%) at cutoff five, while hybrid retrieval with reranking omits it on 14 (1.0%). The two identities differ on 329 of 1,792 resolvable records. With original-question rankings, their top-five checks disagree on 106 records (5.9%). Frozen reader comparisons associate the aligned object’s presence with 28.6 to 31.0 points higher exact match. In a deliberately selected 64-item cohort, removing that passage sharply lowers exact match, while removing a similar-length comparison passage does not reproduce the drop. We release the Returned-Object Profile (ROP), an executable record of the target, returned-ID field, cutoff, membership rule, and complete expected population, with data and an offline replay.

LLM-based scientific agents have shown strong capacity for autonomous research, yet their safety layers remain structurally divorced from core reasoning: they inspect pipeline outputs rather than shaping the deliberation that produces them. This separation opens two failure modes: safety signals accumulated at one stage are discarded before the next, and sequences of individually benign tool calls can compose into harmful outcomes that no single-step filter detects. To address these challenges, we introduce **SciTrace**, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. SciTrace couples two complementary mechanisms: a *Safety-Intrinsic Reasoning Loop* (SIR) that maintains a cumulative risk state across the Thinker, Experimenter, Writer, and Reviewer stages through joint task-and-safety deliberation, and a *Compositional Tool-Chain Verifier* (CTV) that performs trajectory-aware safety checks before execution, catching risks that surface only across multi-step tool sequences. Evaluated on 240 high-risk research tasks and 120 tool-related risk tasks spanning six scientific domains, SciTrace achieves state-of-the-art (**SOTA**) safety among compared frameworks across four backbone models: it consistently improves tool call safety and adversarial robustness while preserving scientific output quality, and it uncovers **78.8%** of the compositional tool-chain escapes that single-step monitors miss. The project website is available at [https://opensciagent.github.io/SciTrace/](https://opensciagent.github.io/SciTrace/).