Asking for more than three letters of recommendation from four professors to reduce the risk of missing letters?
The two different application management systems that I've used at both a public and private R1 (intensive research oriented doctoral granting universities) don't care once you've hit the minimum required -- the application is marked complete if it meets the minimum number of items in that category even if there are other letters that might be pending. 

So it's a good strategy to request more letters than are minimally required because of the strong possibility of professorial flakitude.