Benchmark object detection (OD) datasets play a pivotal role in advancing computer vision applications such as autonomous driving, and surveillance, as well as in training and evaluating deep learning-based state-of-the-art detection models. Among them, MS-COCO has become a standard benchmark due to its diverse object categories and complex scenes. However, despite its wide adoption, MS-COCO suffers from various annotation issues, including missing labels, incorrect class assignments, inaccurate bounding boxes, duplicate labels, and group labeling inconsistencies. These errors not only hinder model training but also degrade the reliability and generalization of OD models. To address these challenges, we propose a comprehensive refinement framework and present MJ-COCO, a newly re-annotated version of MS-COCO. Our approach begins with loss and gradient-based error detection to identify potentially mislabeled or hard-to-learn samples. Next, we apply a four-stage pseudo-labeling refinement process: (1) bounding box generation using invertible transformations, (2) IoU-based duplicate removal and confidence merging, (3) class consistency verification via expert objects recognizer, and (4) spatial adjustment based on object region activation map analysis. This integrated pipeline enables scalable and accurate correction of annotation errors without manual re-labeling. Extensive experiments were conducted across four validation datasets: MS-COCO, Sama COCO, Objects365, and PASCAL VOC. Models trained on MJ-COCO consistently outperformed those trained on MS-COCO, achieving improvements in Average Precision (AP) and APS metrics. MJ-COCO also demonstrated significant gains in annotation coverage: for example, the number of small object annotations increased by more than 200,000 compared to MS-COCO.