It all depends on what the obfuscator does. Proguard is a relatively weak obfuscator - it basically only renames things and strips out unused methods. So running Proguard on the same application twice is pretty much useless, but it won't cause any ill effects.
If you use a stronger obfuscator however, things will almost certainly break. For example, Allatori and Stringer both encrypt constant strings with a key derived from the class and method name of the caller. At runtime, the string decrpytion function uses various hacks to get the name of the caller and then decrypts the string with that.
If you then run Proguard on the obfuscated application, Proguard will blindly rename the classes, meaning that when the string decryption functions are called, the decryption key will be incorrect and the application will get garbage strings at best or much more likely just crash.