Joris Kuipers discusses challenges faced in using CQRS and event sourcing based on his experience with Axon, emphasizing the importance of designing for forwards compatibility, especially when introducing new events. He highlights the complexities involved in deployment strategies, emphasizing the necessity of automated processes and the need for thorough testing. The talk serves as a guide for architects to balance the benefits of CQRS and event sourcing with the architectural trade-offs they entail.