Assembly Reference Manager Question

I am trying to add a custom .dll to a client-side customization. When I add the .dll as a custom assembly, it works fine. However, when I try to go back into the assembly reference manager, it gives me an error saying that my .dll already exists. The customization appears to be functioning correctly with the exception of this error when I open the customization in developer mode and access the assembly reference manager. I also noticed that epicor moved my .dll from the custom assemblies to the native assemblies. Has this ever happened to anyone else?