WebCenter Content Server will deny a check-in when the primary file and the alternate file both have the same file extension. This default behavior is to discourage users from checking the same file in for both the primary and the secondary. Why might they do that? Perhaps they don’t know what the fields really mean?

The primary file should be the original asset. The secondary or alternate file is also called the web viewable file. Examples of proper pairings might include:

1. Microsoft Word as a primary with an Adobe Acrobat PDF as the alternate
2. A ZIP file as the primary and a Readme.txt as the alternate
3. A Photoshop PSD file as the primary and a PNG as the alternate

Sometimes you really need to be able to check in a primary and alternate that have the same file extension. When this is the case you can add this configuration to your config.cfg file:

AllowSamePrimaryAlternateExtensions=true

See the official documentation here:
http://docs.oracle.com/cd/E14571_01/doc.1111/e10726/c06_core_ref010.htm

Other configurations you may find handy:
http://docs.oracle.com/cd/E21043_01/doc.1111/e10726/c04_master_usage004.htm