This paper proposes a two-stage semantic filtering and consistency framework to address the vulnerability of augmented search generation (RAG) systems that leverage external knowledge to corpus contamination and attacks. In the first stage, the entity-intent-relation extractor (EIRE) performs semantic and cluster-based filtering to evaluate the semantic relevance between user queries and filtered documents, selectively adding useful documents to the search database. In the second stage, an EIRE-based consistency filtering module analyzes the semantic consistency between the query, candidate answers, and retrieved knowledge, thereby removing internal and external contradictions that could mislead the model. Through this two-stage process, SeCon-RAG preserves useful knowledge while mitigating contamination-induced contradictions, enhancing the robustness of generation and the reliability of output.