Application.cfm and other cfc includes

I am wondering if having multiple Application.cfm files causes or can cause problems?

Here is what I have:

I have my root(public) folder that contains an Application.cfm file and I also have an 'admin'(private) child folder with a Application.cfm file also. There is also a 'cfc' folder(child of root folder) to handle the normal cfc things. The root folder and admin folder both have pages that call potentially the same cfc files from the cfc folder. Will or can this cause any problems or anomalies by including pages this way? The application.cfm files are exactly the same except for changing the application name. Hopefully I was clear enough in my explanation. TIA.