Continuous glucose monitoring (CGM) data stored in data warehouses often include duplicated or time-shifted uploads from the same patient, compromising data quality and accuracy of resulting CGM metrics. We developed a processing algorithm to detect and resolve these errors. We validated the algorithm using two weeks of CGM data from 2038 patients with diabetes. Duplication errors were identified in 528 patients, with 25.7% showing significant differences in at least one metric (Time in Range, Coefficient of Variation, Glycemic Management Indicator, or Glycemic Episode counts) between raw and processed data. Eleven patients crossed clinically meaningful thresholds in one or more metrics after processing. Our results underscore the importance of real-world CGM data processing to maintain accurate and reliable CGM metrics for research and clinical care.