Everything is fine (including the sorting :-) ), you were just missing out on the third sorting-validation:

"The Components must be ordered by amount of Subcomponents, in descending order"

Just change your final for-loop to and judge gives 100%:

    for (let system of systems) {
        console.log(system.systemName);
        let components = system.components;
        
        for (let component of components.sort((a, b) => b.subcomponents.length - a.subcomponents.length)) {
            console.log(`|||${component.name}`)
            let subcomponents = component.subcomponents;  
            for (const subcomponent of subcomponents) {
                console.log(`||||||${subcomponent}`);
            } 
        }
    }

Or, alternative with Object.values():

function components(array) {

    class System {
        constructor(name) {
            this.systemName = name;
            this.components = [];
        }

        addComponent(component) {
            this.components.push(component);
        }
        get getComponents() {
            return this.components;
        }
    }
    class Component {
        constructor(name) {
            this.name = name;
            this.subcomponents = [];
        }
        addSubComponent(subcomponent) {
            this.subcomponents.push(subcomponent);
        }
    }

    let systems = [];

    for (let i = 0; i < array.length; i++) {
        let elements = array[i].split(' | ');
        let containsInSystems = (systemName) => {
            let system = null;
            systems.forEach(el => el.systemName === systemName ? system = el : null);
            return system;
        }

        if (containsInSystems(elements[0]) === null) {
            let system = new System(elements[0]);
            let component = new Component(elements[1]);
            component.addSubComponent(elements[2]);
            system.addComponent(component);
            systems.push(system);
        } else {
            let system = containsInSystems(elements[0]);

            let component = system.getComponents.find(el => el.name === elements[1]);

            if (component !== undefined) {
                component.addSubComponent(elements[2]);
            } else {
                let newComponent = new Component(elements[1]);
                newComponent.addSubComponent(elements[2]);
                system.addComponent(newComponent);
            }
        }
    }

    // systems = systems.sort(function (a, b) {
    //     if (a.components.length > b.components.length) { return -1; }
    //     if (a.components.length < b.components.length) { return 1; }
    //     if (a.systemName > b.systemName) { return 1; }
    //     if (a.systemName < b.systemName) { return -1; }
    //     else { return 0; }
    // });

    systems = Object.values(systems).sort((a, b) => {
        return b.components.length - a.components.length || a.systemName.localeCompare(b.systemName);
    });

    // for (let system of systems) {
    //     console.log(system.systemName);
    //     let components = system.components;

    //     for (let component of components.sort((a, b) => b.subcomponents.length - a.subcomponents.length)) {
    //         console.log(`|||${component.name}`)
    //         let subcomponents = component.subcomponents;
    //         for (const subcomponent of subcomponents) {
    //             console.log(`||||||${subcomponent}`);
    //         }
    //     }
    // }

    for (let system of Object.values(systems)) {
        console.log(system.systemName);
        let components = system.components;

        for (let component of components.sort((a, b) => b.subcomponents.length - a.subcomponents.length)) {
            console.log(`|||${component.name}`)
            let subcomponents = component.subcomponents;
            for (const subcomponent of subcomponents) {
                console.log(`||||||${subcomponent}`);
            }
        }
    }
}

Best,

great job! i l love it!  couples therapy san diego