Synthetic data has become essential for training foundation models, yet benchmark contamination threatens evaluation integrity. Although existing detection methods identify token-level overlap, they fail to detect semantic-level contamination where synthetic data conceptually resemble benchmarks without lexical overlap. This gap is critical as foundation models increasingly train on synthetic data that may implicitly encode benchmark knowledge. We propose a hierarchical contamination detection framework operating at four levels: token level, semantic level, reasoning pattern, and performance cliff detection. Through controlled experiments on MMLU, GSM8K and HumanEval, we demonstrate that semantic-level contamination evades existing methods (F1=0.17-0.49) but is effectively detected by our hierarchical approach (F1 = 0.76), with an average improvement of 26. 5\% over state-of-the-art baselines. Our framework provides practitioners with practical tools for audit pipelines and enables responsible deployment of synthetic training data.