When Data Quality Issues Collide: A Large-Scale Empirical Study of Co-Occurring Data Quality Issues in Software Defect Prediction

Software Defect Prediction (SDP) models are central to proactive software quality assurance, yet their effectiveness is often constrained by the quality of available datasets. Prior research has typically examined single issues such as class imbalance or feature irrelevance in isolation, overlooking that real-world data problems frequently co-occur and interact. This study presents, to our knowledge, the first large-scale empirical analysis in SDP that simultaneously examines five co-occurring data quality issues (class imbalance, class overlap, irrelevant features, attribute noise, and outliers) across 374 datasets and five classifiers. We employ Explainable Boosting Machines together with stratified interaction analysis to quantify both direct and conditional effects under default hyperparameter settings, reflecting practical baseline usage. Our results show that co-occurrence is nearly universal: even the least frequent issue (attribute noise) appears alongside others in more than 93% of datasets. Irrelevant features and imbalance are nearly ubiquitous, while class overlap is the most consistently harmful issue. We identify stable tipping points around 0.20 for class overlap, 0.65-0.70 for imbalance, and 0.94 for irrelevance, beyond which most models begin to degrade. We also uncover counterintuitive patterns, such as outliers improving performance when irrelevant features are low, underscoring the importance of context-aware evaluation. Finally, we expose a performance-robustness trade-off: no single learner dominates under all conditions. By jointly analyzing prevalence, co-occurrence, thresholds, and conditional effects, our study directly addresses a persistent gap in SDP research. Hence, moving beyond isolated analyses to provide a holistic, data-aware understanding of how quality issues shape model performance in real-world settings.