Challenges in Power BI integration include data incompatibility, latency, and security concerns. These are resolved by employing data transformation tools like Power Query, which standardized formats. Latency issues are addressed through optimized queries and efficient ETL pipelines. Security is enhanced using encryption, role-based access controls, and compliance measures. Testing and continuous monitoring ensure stable integrations. Additionally, Power BI development leveraging APIs and middleware bridges gaps between incompatible systems, delivering a seamless and robust integration process for businesses.