JS uncaught reference error, ...

There are no such conflicts between JavaScript references. You are just trying to dereference undefined object. This is a special object specific to JavaScript, distinct from null and all other values. It is used by the runtime system when you declare some variable but don't initialize it. Also, you can assign undefined to any other object at any time.

Consider this:

var Cookie; // undefined
Cookie = undefined; // same as above

function A() { alert("Do something"); }
Cookie = A(); // A did not return anything,
// so Cookie is still undefined

// Now, consider this:
var someOtherVariable = Cookie; // fine!

// But exception if thrown if 
var someOtherVariable = Cookie.a;

I tried it on Mozilla and Chrome, it actually throws TypeError with this error message, but I can imagine that some other browser throws different exception object. Reference errors come in different situations, when some variable (f in my example below) is not even declared:

var someOtherVariable = f;
// ReferenceError: f is not defined

On undefined object (primitive value), please see: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/undefined[^],
not to be confused with null: https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/null[^].

Remaining exception you described is "not a function". Consider this example:

var Element = { }; //value empty object
Element.extend = 42; //fine

Element.extend();
// TypeError:
// Element.extend is not a function

// Another possibility is this:
Element.somethingNotCreated();
// TypeError:
//Element.somethingNotCreated is not a function

I hope the exception message is self-explained.

Please don't ask me what your code did wrong; I don't know and, frankly, don't want to know. You just need to understand the first principles, than you can dig it out.

—SA