A sample which shows that you cannot stub the `Array.prototype.filter` method. All works fine for `Array.prototype.map`.

sinon-array-test.js

'use strict';

const sinon = require( 'sinon' );
const expect = require( 'chai' ).expect;

describe( 'Array.prototype', () => {
	describe( 'map()', () => {
		it( 'uses native map', () => {
			const callback = sinon.spy();
			const stub = sinon.stub( Array.prototype, 'map' ).returns( [ 2, 4 ] );

			const arr = [].map( callback );

			expect( stub.calledOnce ).to.equal( true );
			expect( stub.firstCall.args[ 0 ] ).to.equal( callback );
			expect( arr ).to.deep.equal( [ 2, 4 ] );
		} );
	} );

	describe( 'filter()', () => {
		it( 'uses native filter', () => {
			const callback = sinon.spy();
			const stub = sinon.stub( Array.prototype, 'filter' ).returns( [ 1 ] );

			const arr = [].filter( callback );

			expect( stub.calledOnce ).to.equal( true );
			expect( stub.firstCall.args[ 0 ] ).to.equal( callback );
			expect( arr[ 0 ] ).to.equal( 1 );
		} );
	} );
} );