Execution-based evaluation of LLM-generated code implicitly treats successful execution as a proxy for correctness. In scientific simulation, this proxy is insufficient: a generated input file can run, mesh, and converge while encoding governing equations that differ from the user's intent. We call this mismatch between intended physics and generated code the comprehension-generation gap. We instantiate this in MOOSE, where Kernel and BC objects map compositionally to weak-form residual terms, enabling deterministic reconstruction of the encoded PDE and comparison against an intended contract. We formalize this comparison as the Intent Fidelity Score (IFS), a structural metric covering governing terms, BCs, ICs, coefficients, and time scheme. Building on IFS, we develop a PDE-grounded refinement loop that uses deterministic violation reports to correct generated code iteratively. We evaluate on MooseBench, a 220-case multiphysics benchmark with PDE-level ground truth released with this work. On this benchmark, our method consistently improves mean IFS over direct generation, with gains concentrated on hard cases. On the subset where direct generation falls below IFS 0.7, refinement adds +0.22 to +0.41 absolute IFS. In the deployment audit, execution-only repair improves execution success while leaving 39-40% of all 220 cases runnable but still solving the wrong physics across the three main deployment-audit models, exposing executability and intent fidelity as separable failure modes. Static proof-of-concept experiments on four PDE-oriented DSLs (UFL/FEniCS, FreeFEM, FiPy, and Devito) suggest that the reconstruction-and-comparison pattern extends beyond MOOSE. These findings reinforce that executable simulation code should be verified against the mathematical structure it is intended to encode, not accepted on execution alone.