Scientific Workflow Systems (SWSs) such as Nextflow have become essential software frameworks for conducting reproducible, scalable, and portable computational analyses in data-intensive fields like genomics, transcriptomics, and proteomics. Building on Nextflow, the nf-core community curates standardized, peer-reviewed pipelines that follow strict testing, documentation, and governance guidelines. Despite its widespread adoption, little is known about the challenges users face in developing and maintaining these pipelines. This paper presents an empirical study of 25,173 issues and pull requests from these pipelines to uncover recurring challenges, management practices, and perceived difficulties. Using BERTopic modeling, we identify 13 key challenges, including pipeline development and integration, bug fixing, integrating genomic data, managing CI configurations, and handling version updates. We then examine issue-resolution dynamics, showing that 89.38\% of issues and pull requests are eventually closed, with half resolved within 3 days. Statistical analysis reveals that the presence of labels (large effect, $\mathit{d} = 0.94$) and code snippets (medium effect, $\mathit{d} = 0.50$) significantly improves the likelihood of resolution. Further analysis reveals that tool development and repository maintenance poses the most significant challenges, followed by testing pipelines and CI configurations, and debugging containerized pipelines. Overall, this study provides actionable insights into the collaborative development and maintenance of nf-core pipelines, highlighting opportunities to enhance their usability, sustainability, and reproducibility.