Even if their implementation is identical to the standard, it is still problematic. The key problem is the way MooTools tries to copy over that method (and many other methods):

> Currently, Array.prototype.flatten = mooToolsFlattenImplementation creates an enumerable flatten property, so it’s later copied to Elements. But if we ship a native version of flatten, it becomes non-enumerable, and isn’t copied to Elements. Any code relying on MooTools’ Elements.prototype.flatten is now broken.

> Although it seems like changing the native Array.prototype.flatten to be enumerable would fix the problem, it would likely cause even more compatibility issues. Every website relying on for-in to iterate over an array (which is a bad practice, but it happens) would then suddenly get an additional loop iteration for the flatten property.

> The bigger underlying problem here is modifying built-in objects. Extending native prototypes is generally accepted as a bad practice nowadays, as it doesn’t compose nicely with other libraries and third-party code. Don’t modify objects you don’t own!