Automated Program Repair (APR) agents leverage large language models (LLMs) to autonomously diagnose and patch software bugs using planning, reasoning, and tools. Although these agents show strong performance on leaderboards such as SWE-bench, little is understood about how they take actions, where they fail, and how their behavior compares to human developers. In this paper, we present the first systematic analysis of these limitations using 5 state-of-the-art APR agents. We trace the full decision-making pipelines of the 5 APR agents across 500 real-world repair tasks, from issue description to patch validation. Our study reveals that, while agents excel at simple fixes, they struggle with logic-intensive bugs, often generating verbose, overfitted patches that pass existing test suites without solving the root cause. Test generation and regression test selection remain major bottlenecks, as agents fail to reproduce issues or run relevant regression tests. Moreover, many agents operate with primitive tooling (e.g. bash scripts) and do not have access to debuggers or program analysis tools. These findings highlight key limitations of current APR systems and motivate several directions for next-generation APR design, including but not limited to: (1) a shift-left approach emphasizing early, high-quality test generation and validation to reduce spurious fixes and improve semantic correctness; (2) richer, more integrated tool ecosystems; (3) diversified agent architectures that combine complementary strengths; and (4) benchmarks that prioritize semantic repair quality and test-generation fidelity over surface-level success metrics.

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