Pairwise evaluation of large language models (LLMs) has become the dominant paradigm for benchmarking open-ended tasks, yet non-transitive preferences—where evaluators prefer A over B, B over C, but C over A—fundamentally undermine ranking reliability. We show that this critical issue stems largely from low-quality data that contains inherently ambiguous preference pairs. To address this challenge, we propose ELSPR, a principled graph-theoretic framework that models pairwise preferences as tournament graphs and systematically identifies problematic training data. ELSPR quantifies non-transitivity through strongly connected components (SCCs) analysis and measures overall preference clarity using a novel normalized directed graph structural entropy metric. Our filtering methodology selectively removes preference data that induce non-transitivity while preserving transitive preferences. Extensive experiments on the AlpacaEval benchmark demonstrate that models fine-tuned on ELSPR-filtered data achieve substantial improvements: a 13.8\% reduction in non-transitivity, a 0.088 decrease in structural entropy, and significantly enhanced discriminative power in real-world evaluation systems. Human validation confirms that discarded data exhibit dramatically lower inter-annotator agreement (34.4\% vs. 52.6\%) and model-human consistency (51.2\% vs. 80.6\%) compared to cleaned data. These findings establish ELSPR as an effective data self-purification approach for developing more robust, consistent, and human-aligned LLM evaluation systems.