JSFiddle - React, Tailwind, and code Playground

JavaScript

function index(arr) {
    return arr.reduce(function(acc, item){
        return acc[JSON.stringify(item.sort())] = item, acc
    }, {})    
}
var arrayA = [[0,1], [2,0], [0,3], [4,0], [0,5]];

var arrayB = [[1,0], [0,3]];

var indexB = index(arrayB);

arrayA = arrayA.filter( function( el ) {
  return !(JSON.stringify(el.sort()) in indexB);
} );

console.log(arrayA);