The common pitfalls of migrating to cloud native setups in large enterprises include a lack of clear structure and governance, leading to chaos and disorganization among teams. As operations are decentralized and teams start building their own infrastructure, the complexity increases, and it becomes difficult for developers to manage their environments. The transition can take up to 2 years, with phases including a period of innovation, followed by operational challenges, and finally, the adoption of a platform model to bring order and structure back to the organization. By understanding these common pitfalls, organizations can learn how to mitigate them and establish a successful cloud native migration strategy.