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Software Ecosystem (SECO) has emerged as a crucial concept, which represents a collaborative and interconnected environment in which a variety of actors engage in developing software systems. SECOs play a key role in the development of Cyber-Physical Systems (CPSs), that present a myriad of challenges, primarily due to the need for real-time responsiveness, reliability, security, and interoperability. The implications of leveraging SECOs for developing CPSs are profound in both research and practice. This paper aims to understand the collaboration between industry and academia within SECOs for the development of CPSs, identifying potential challenges and providing insights and guidelines for the proper management of these collaborations. We conducted a systematic literature review (SLR), complemented by empirical evidence collected through an opinion survey administered to the partners of the European collaborative project AIDOaRt, a concrete example of a SECO, which worked on the development of CPSs. From these findings we discuss the identified challenges, and potential effects on collaboration, in addition to our lessons learned in the AIDOaRt project and SECO.