Software defect prediction (SDP) utilizes the learning models to detect the defective modules in project, and their performance depends on the quality of training data. The previous researches mainly focus on the quality problems of class imbalance and feature redundancy. However, training data often contain some instances that belong to different class but have similar values on features, and this leads to class overlap to affect the quality of training data. Our goal is to investigate the impact of class overlap on software defect prediction. At the same time, we propose an improved K-Means clustering cleaning approach (IKMCCA) to solve both the class overlap and class imbalance problems. Specifically, we check whether K-Means clustering cleaning approach (KMCCA) or neighborhood cleaning learning (NCL) or IKMCCA is feasible to improve defect detection performance for two cases (i) within-project defect prediction (WPDP) (ii) cross-project defect prediction (CPDP). To have an objective estimate of class overlap, we carry out our investigations on 28 open source projects, and compare the performance of state-of-the-art learning models for the above-mentioned cases by using IKMCCA or KMCCA or NCL VS. Without cleaning data. The experimental results make clear that learning models obtain significantly better performance in terms of balance, Recall and AUC for both WPDP and CPDP when the overlapping instances are removed. Moreover, it is better to consider both class overlap and class imbalance.