You can have an issue at the application layer, but most issues you encounter happen at the other layers. However, some issues in the application layer or in other layers (depending on how you look at them) include items such as the following:
Software bugs, such as an application that crashes when sending data too quickly. When things like this happen, all you can do is diagnose the issue, contact the software manufacturer, reduce the occurrence of the issues by adjusting other configuration elements, or change to an equivalent application if one is available.
Incorrect settings, such as host names or addresses, that may have changed and have not been documented. Find out what the correct settings should be, even if it means double-checking client and server configurations.
Services are bound to an incorrect port, such as one running Remote Desktop Protocol (RDP) services or HTTP services on non-standard ports. You may be able to get to the remote host, for example, but if you try to talk to the wrong port, you cannot connect.
It is not uncommon for internal use servers to have multiple websites installed on them, with only one of them being allowed to run on the standard HTTP port of 80. Also, some IT administrators choose to run the RDP service on a non-standard port to keep unauthorized users from attempting to connect to the RDP service.
The client or server components that you use do not follow the published standards for the protocol. Sometimes custom written code does not honor published protocols and can cause lengthy troubleshooting exercises. In one case the problem was only identified by reading published standards and capturing network traffic with the Wireshark network capture tool.
Some companies that implement devices have taken liberties with implementing protocols and the features they support. This makes achieving compatibility with other devices from other vendors difficult and can be considered an application problem that is often resolved only after you change the client or server software that you use.
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Source:http://www.dummies.com/how-to/content/cisco-networking-application-layer-troubleshooting.html
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