What are the major pain points of a software agency?

Two biggest challenges I have faced - Timely payments & Requesting major changes after product is ready. Timely payments: Most clients prefer making payments in parts based on the status of completion, which is not a bad thing. But in my case, whenever I went lenient and completed the project based on the trust that the payment will arrive later. I was always let down by the client. Requesting major changes: Clients don't always understand the effort required for a change. Therefore I always recommend having a clear agreement stating the scope of work. And also including cost for any major changes. Clear communication is a must have. Don't shy out ever!