They had massive problems with their main database cluster (MySQL). If you read through their engineering blog, most of the outages were related to their growth and the main database cluster. They moved workloads for some features to different clusters, but that's only to buy more time. Eventually they'll do proper shredding (by user or org I guess, not by feature) but that takes time.
Their engineering blog is full of articles about MySQL and the main "mysql1" database cluster, e.g. https://github.blog/2021-09-27-partitioning-githubs-relation...