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Active learning is widely used in materials discovery to reduce the number of expensive density functional theory calculations required for surrogate-model training. Its dominant acquisition rule, uncertainty sampling, assumes that the most uncertain configuration will also yield the greatest information gain. Although this logic performs well for many bulk properties, it breaks down for defect formation energies. In this setting, uncertainty sampling repeatedly selects uninformative structures, misallocates computational budget, and fails to reach the defective configurations that govern vacancy, interstitial, and substitutional behavior in technologically important materials. This failure reflects a structural mismatch between the acquisition rule and defect physics. Defect configurations are rare in configuration space, energetics are highly localized, and DFT labels often contain substantial aleatoric noise from finite-size effects, charge corrections, and supercell artifacts. These conditions weaken the link between predictive uncertainty and useful learning signal, while representation bias in models trained mainly on perfect crystals further erodes selectivity. This study develops a failure-mode analysis of uncertainty sampling for defect formation energies, identifying recurrent breakdowns in sampling, representation, calibration, and budget use. It also outlines practical detection principles and defect-aware mitigation strategies, including initialization with defective structures, hybrid acquisition functions, epistemic-only scoring, and budget partitioning. The central implication is that active learning for defect discovery cannot rely on generic uncertainty-based querying. Effective acceleration in this domain requires acquisition strategies designed around the rarity, locality, and noise structure of defect energetics.