Not empty array doesn't contain its element:
var a = [,];
a.length; //1, some element exists
a.indexOf(a[0]); //-1
// We have the array with non-zero length, which doesn't contain its first element. WTF?
The problem is in this:
a[0] is undefined. undefined is the javascript primitive type. But when we init an array
the ES5 spec tells us the following about array initialisers:
Elided array elements are not defined.
...
The missing array element contributes to the length of the Array and increases the index of subsequent elements.
Elements are not undefined, they are not initialized.
When we invoke indexOf on an array this is one of the steps that happens:
Let kPresent be the result of calling the [[HasProperty]] internal method of O with argument ToString(k).
In that, k is a number corresponding to an array index and O is the array itself.
Since elided elements were not defined the array does not have a property for the corresponding index.
Ok. But why do we get undefined when get the first array element?
Javascript is a prototype-based scripting language and Array is an object, too.
So if there is no property 0 in an array, the internal engine goes deeper to the prototype
and there is no such property in the prototype chain - return undefined.
When we try to access the value 0 property of array the internal method [[GetProperty]] gets called.
If there is no such property [[GetProperty]] we try to get it from the prototype chain
and undefined is returned if it stops on null (end of prototype chains).