Raycaster, not registering certain objects

Questions
2

native raycasting with three.js is not optimized, and check every triangles in the scene.
your raycaster/renderer code is not optimized either. The version below work better (less triangles, larger sphere), but still fail after few minutes (some memory leak). Try to start from a clean official example instead.

If you need some extreme raycasting I suggest using three-mesh-bvh instead.

here is my half-working version, you can paste this inside a blank https://codepen.io/pen/

import * as THREE from "https://cdn.skypack.dev/three@0.139.2";

const renderer = new THREE.WebGLRenderer({ alpha: true });
renderer.setSize(window.innerWidth, window.innerHeight);
document.body.appendChild(renderer.domElement);

var pointer, raycaster;
pointer = new THREE.Vector2();
raycaster = new THREE.Raycaster();
pointer.x = 1;
pointer.y = 1;

const scene = new THREE.Scene();
renderer.setPixelRatio(window.devicePixelRatio);
renderer.setSize(window.innerWidth, window.innerHeight);
const camera = new THREE.PerspectiveCamera(
    45,
    window.innerWidth / window.innerHeight,
    1,
    10000
);

camera.position.set(0, 200, 1000);
renderer.render(scene, camera);

window.addEventListener("pointermove", onPointerMove);

/* lighting */

const pointLight = new THREE.PointLight(0xffffff);
pointLight.position.set(-500, 500, 1000);
scene.add(pointLight);

//
//
// main
//
//

/* world */

const worldTexture = new THREE.TextureLoader().load("./assets/world-map.jpg");
const world = new THREE.Mesh(
    new THREE.SphereGeometry(100, 10, 10),
    new THREE.MeshStandardMaterial({
        map: worldTexture,
        // wireframe: true,
    })
);
scene.add(world);

/* ellipse const */
const ellipseMaterial = new THREE.LineBasicMaterial({ color: 0x000000 });

/* ellipse two */

const curveTwo = new THREE.EllipseCurve(
    0,
    0, // ax, aY
    150,
    150, // xRadius, yRadius
    0,
    2 * Math.PI, // aStartAngle, aEndAngle
    false, // aClockwise
    0 // aRotation
);

const pointsTwo = curveTwo.getPoints(100);
const geometryTwo = new THREE.BufferGeometry().setFromPoints(pointsTwo);

// Create the final object to add to the scene
const ellipseTwo = new THREE.Line(geometryTwo, ellipseMaterial);
ellipseTwo.rotation.x = Math.PI * 0.5;
ellipseTwo.rotation.z = Math.PI * 1.5;
ellipseTwo.rotation.y = Math.PI * 0.05;

scene.add(ellipseTwo);

/* comet */

const cometTwo = new THREE.Mesh(
    new THREE.SphereGeometry(50, 50, 5),
    new THREE.MeshStandardMaterial({
        //wireframe: true,
    })
);

scene.add(cometTwo);

/* ellipse three */

const curveThree = new THREE.EllipseCurve(
    50,
    0, // ax, aY
    250,
    150, // xRadius, yRadius
    0,
    2 * Math.PI, // aStartAngle, aEndAngle
    false, // aClockwise
    0 // aRotation
);

const pointsThree = curveThree.getPoints(100);
const geometryThree = new THREE.BufferGeometry().setFromPoints(pointsThree);

// Create the final object to add to the scene
const ellipseThree = new THREE.Line(geometryThree, ellipseMaterial);
ellipseThree.rotation.x = Math.PI * 0.6;
ellipseThree.rotation.y = Math.PI * 0.15;

scene.add(ellipseThree);

/* comet */

const cometThree = new THREE.Mesh(
    new THREE.SphereGeometry(50, 50, 5),
    new THREE.MeshStandardMaterial({
        //wireframe: true,
    })
);
cometThree.position.x = 200;

scene.add(cometThree);

/* clock */
let clock = new THREE.Clock();
let v = new THREE.Vector3();
let w = new THREE.Vector3();

/* function */
console.log("scene children", scene.children);

animate();

function animate() {
    requestAnimationFrame(animate);
    let s = (clock.getElapsedTime() * 0.08) % 1;
    let t = (clock.getElapsedTime() * 0.05) % 1;

    curveTwo.getPointAt(s, v);
    cometTwo.position.copy(v);
    cometTwo.position.applyMatrix4(ellipseTwo.matrixWorld);

    curveThree.getPointAt(t, w);
    cometThree.position.copy(w);
    cometThree.position.applyMatrix4(ellipseThree.matrixWorld);

    hoverElement();

    world.rotation.y += -0.001;

    renderer.render(scene, camera);
}

function onPointerMove(event) {
    pointer.x = (event.clientX / window.innerWidth) * 2 - 1;
    pointer.y = -(event.clientY / window.innerHeight) * 2 + 1;
}

function hoverElement() {
    raycaster.setFromCamera(pointer, camera);
    const intersects = raycaster.intersectObjects(scene.children);

    if (intersects.length > 0) {
        console.log("current intersects", intersects);
    }
}