# When Agents Implement Systems: A Case Study in Defects, Detection, and Evaluation Rigor

arXiv: https://arxiv.org/abs/2609.01985 · HTML: https://mlsanity.com/paper/2609.01985/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Software engineering coding agents, one of 16 directions in LLM agents and tool use.
- Builds on 5 of its 10 references that are in the map.
- First posted on arXiv 2 Sep 2026.

## Placed in

- LLM agents and tool use / [Software engineering coding agents](https://mlsanity.com/agents/software-engineering-coding-agents/)

## Builds on (most cited first, 5 of 5)

- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [HotpotQA: A Dataset for Diverse, Explainable Multi-hop Question Answering](https://mlsanity.com/paper/1809.09600/) (2018)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [From Local to Global: A Graph RAG Approach to Query-Focused Summarization](https://mlsanity.com/paper/2404.16130/) (2024)

## Abstract (arXiv)

As LLM coding agents increasingly perform end-to-end engineering work, we lack empirical characterization of how they behave on systems-level requirements: schema design, async orchestration, configuration correctness, and retrieval-filtering trade-offs. We present a case study of one such agent implementing a multi-component data system against a detailed pre-existing specification. Storage technologies, schema, entity-resolution algorithm, and retrieval-filtering strategy were fixed in advance; the agent autonomy was in the implementation, in diagnosing and fixing defects it introduced, and in interaction-design choices left open. Over a single session, we catalog five such defects, categorized by constraint violated and detection method. We further evaluate, on the public HotpotQA benchmark, the one retrieval trade-off specified in that architecture: restricting candidates to a graph-identified entity set before ranking versus unfiltered search. We substitute the benchmark gold evidence labels for entity identification, since we lacked LLM access to run that stage, and report standard recall rather than the benchmark own accuracy metrics. Across retrieval budgets from 1 to 10 and 100 questions against a pooled corpus of 2994 paragraphs, filtered recall reaches its ceiling by a budget of 3, expected once candidates are restricted to the gold paragraphs themselves, while unfiltered search recovers all required evidence only 69 percent of the time even at a budget of 10, a gap that holds at every budget tested, with sign test p less than 0.0001. We close with a discussion of where the agent autonomy succeeded versus required correction, including one instance where a claimed performance fix was never re-measured on the regression that motivated it.