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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 \\textbf{SciTrace}, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. 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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 \\textbf{SciTrace}, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. 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