Software ecosystems (SECO) play a crucial role in modern software development by enabling accelerated innovation, collaboration among multiple stakeholders, and efficient utilization of shared resources and technologies. However, achieving these benefits requires robust, adaptable, and well-structured architectural design and management. Despite their importance, SECO architectures face several critical challenges, including interface instability, security vulnerabilities, scalability limitations, governance complexity, sustainability concerns, and evolving ecosystem dynamics. Although prior studies have explored individual aspects of SECO, there is a clear research gap in providing a comprehensive and systematic synthesis of architectural challenges and their corresponding mitigation strategies. In particular, no systematic literature review (SLR) has thoroughly examined these issues in an integrated manner. To address this gap, this study aims to systematically identify, categorize, and analyze architectural challenges in SECO and evaluate existing mitigation techniques. A structured SLR methodology is employed to collect, assess, and synthesize relevant literature, leading to the development of a conceptual framework that organizes both challenges and solutions. The findings reveal that key mitigation strategies—such as modularization, variability management, custom design approaches, and sandboxing—can significantly improve architectural stability, scalability, and sustainability. These results provide valuable insights for both researchers and practitioners by offering a consolidated understanding of SECO architectural issues and practical guidance for designing more resilient and sustainable software ecosystems.