Quantum compilers face the test oracle problem, judged by an output-equivalence oracle: the compiled circuit must compute the same unitary as the original, modulo global phase and a qubit-layout permutation. This oracle, by construction, checks only that semantic map, not the circuit's own layout, permutation, or phase records: a defect there, or in a fixed-seed run's determinism, can pass unseen though the record is public. This empirical software engineering study of quantum transpiler correctness uses repository mining to measure how often this happens in real merged compiler fixes: a systematically identified corpus of Qiskit transpiler bug-fixes, classified by an independently dual-coded, source-validated fault-manifestation taxonomy. Nineteen of 68 fixes (28%, 95% Wilson CI 19-40%) repair faults invisible to this equivalence screen, even one augmented with compilation-validity, circuit-quality, and performance checks, and an extended 104-fix corpus over a wider window holds at the same rate with a tighter interval (29/104, 27.9%, CI 20-37%). A conservative floor remains even restricted to the one unconditionally equivalence-invisible channel (a corrupted layout or permutation record): 10 of 68 fixes (15%, CI 8-25%) beneath the 28% headline. The gap is not Qiskit-specific: it replicates in tket (7/21, 33%), with Cirq smaller but consistent. We detected no systematic differences on five inexpensive PR-level characteristics (19 vs 49, underpowered alone; the extended 29-vs-75 corpus tightens every interval toward zero). This class dominates the invisible set, concentrating at representation-boundary crossings. We release the corpus, codebook, and coding artifacts for quantum software testing research. Here we only measure it.

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