"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To examine common patterns among different computer-aided diagnosis (CAD) models for Alzheimer's disease (AD) using structural MRI data and to characterize the clinical and imaging features associated with their misclassifications. Materials and Methods This retrospective study utilized 3258 baseline structural MRIs from five multisite datasets and two multidisease datasets collected between September 2005 and December 2019. The 3D Nested Hierarchical Transformer (3DNesT) model and other CAD techniques were utilized for AD classification using 10-fold cross-validation and cross-dataset validation. Subgroup analysis of CAD-misclassified individuals compared clinical/neuroimaging biomarkers using independent t tests with Bonferroni correction. Results This study included 1391 patients with AD (mean age, 72.1 ± 9.2 years, 757 female), 205 with other neurodegenerative diseases (mean age, 64.9 ± 9.9 years, 117 male), and 1662 healthy controls (mean age, 70.6 ± 7.6 years, 935 female). The 3DNesT model achieved 90.1 ± 2.3% crossvalidation accuracy and 82.2%, 90.1%, and 91.6% in three external datasets. Further analysis suggested that false negative (FN) subgroup (n = 223) exhibited minimal atrophy and better cognitive performance than true positive (TP) subgroup (MMSE, FN, 21.4 ± 4.4; TP, 19.7 ± 5.7; PFWE < 0.001), despite displaying similar levels of amyloid beta (FN, 705.9 ± 353.9; TP, 665.7 ± 305.8; PFWE = 0.47), Tau (FN, 352.4 ± 166.8; TP, 371.0 ± 141.8; PFWE = 0.47) burden. Conclusion FN subgroup exhibited atypical structural MRI patterns and clinical measures, fundamentally limiting the diagnostic performance of CAD models based solely on structural MRI. ©RSNA, 2025.