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:
See the official documentation here:
Other configurations you may find handy: