This paper seeks to address the dense labeling problems where a significant fraction of the dataset can be pruned without sacrificing much accuracy. We observe that, on standard medical image segmentation benchmarks, the loss gradient norm-based metrics of individual training examples applied in image classification fail to identify the important samples. To address this issue, we propose a data pruning method by taking into consideration the training dynamics on target regions using Dynamic Average Dice (DAD) score. To the best of ourknowledge, we are among the first to address the data importance in dense labeling tasks in the field of medical image analysis, making the following contributions: (1) investigating the underlying causes with rigorous empirical analysis, and (2) determining effective data pruning approach in dense labeling problems. Our solution can be used as a strong yet simple baseline to select important examples for medical image segmentation with combined data sources.