Reasoning is central to ReAct-based programming agents, yet whether and how they reason about code remains unclear. We study 7,955 issue-resolution trajectories from six single- and multi-agent scaffolds across four programming languages on SWE-bench-Verified, SWE-bench-Pro, and SWE-bench-Lite. We identify 12 forms of code reasoning in 66.95% of trajectories. Code reasoning is associated with higher resolution rates, and its intensity increases with task complexity. However, it remains largely unguided: agents may focus on surface-level symptoms during localization, fail to refine near-correct patches, overlook issue requirements, and generate tests with limited behavioral diversity. To address these limitations, we propose DeskCheck, an agentic scaffold that systematically guides code reasoning throughout repository-level issue resolution. DeskCheck simulates execution paths to localize root causes, simulates candidate patches to refine near-misses, audits patches against issue requirements, and reasons about corner-case inputs and expected outputs before generating tests. On 731 SWE-bench-Pro instances, DeskCheck improves resolution rates over mini-SWE-Agent and Claude Code by 6.29% to 10.53%, at an additional cost of $0.02-$0.28 per instance (average: $0.14). Per-phase analyses show higher method-level localization recall, more successful repairs of imprecisely localized issues, and better detection of missed corner cases in near-correct patches. Exact McNemar tests show statistically significant improvements across all subject LLMs (p < 10^-10), while repeated experiments support robustness to agent nondeterminism. These findings motivate systematic code reasoning as a means of improving programming agents.

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