Online user feedback has become an essential mechanism for software organizations to gain insight into user concerns and to recognize areas for improvement. In software platform ecosystems, staying abreast of user feedback is particularly challenging due to the multitude of feedback channels and the complex interplay with third party applications. In this paper we report from a mixed-method study of user feedback from over 40,000 relevant reviews from 139 SECO platforms out of 2.4 million online user reviews scraped from 283 retrieved SECO platforms. Through thematic analysis and machine learning classifiers with high accuracy, we identified and analyzed six categories of user challenges in the areas of Integration, Customer Support, Design & Complexity, Privacy & Security, Cost & Pricing, and Performance & Compatibility. Our analysis also shows a significant growth of SECO user feedback in the past five years, highlighting the importance of understanding such user feedback as well as research methodologies to automatically study online user concerns in software ecosystems. To further understand mitigation strategies for challenges reported by end users, we interviewed four executives from large ecosystems and describe strategies in addressing those identified challenges. This research is a first large scale study of user feedback in software ecosystems; the categories of user concerns are hopefully useful in guiding platforms in designing and fostering better software ecosystems. Our methodology for automatically classifying the user feedback that is SECO-related can also serve as guidance for future studies that can further advance our understanding of user feedback and how to integrate it into improved software ecosystems.