It's a vast question and really tough to predict exact errors what you will face. Because it's depends on your application adn so many other factors. But we can give some input like where you could expect some errors.
If you develop applications using NWDI setup there you might face some issues in moving the Development objects from One environment to another. Some exceptions yo will see in developing your web dynpro applications this is because of your code or some issues with SAP FM. You may face some difficulties in Web Dynpro componensts integration. May be you will see some SAP Portal related issues and security related when you integrate your application in sap portal.
Here some help on How to handle Error in Web Dynpro java:
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