Large language models (LLMs) are increasingly used for codebook-based content analysis in computational social science, where codebooks translate theoretical concepts into labeling schemes. While prior work reports strong predictive performance, it remains unclear whether these systems produce reliable and robust text annotations. We conduct a large-scale empirical failure-mode analysis of LLM-based coding pipelines across four datasets and five models by systematically evaluating their stability, robustness, and conceptual validity under controlled perturbations, domain shifts, and optimization procedures. We uncover multiple failure modes that are largely invisible under standard metrics, showing that high aggregate scores frequently coexist with severe label-level disparities, instability across runs, domain sensitivity, and shifts in label interpretation. Importantly, these failure modes persist under widely used optimization strategies and remain largely invisible under standard metrics such as accuracy and micro-F1. Our results demonstrate that current LLM-based coding pipelines cannot be treated as stable measurement tools without targeted validation beyond aggregate performance.

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