Fixed that with a simple

width: Math.max(implicitWidth, scrollView.availableWidth)

on the columnlayout

import QtQuick 2.7
import QtQuick.Controls 2.2
import QtQuick.Layouts 1.0

ApplicationWindow {
    id: window
    visible: true
    RowLayout {
        anchors.fill: parent
        Button {}
        ToolSeparator {}
        ScrollView {
            Layout.fillHeight: true
            Layout.alignment: Qt.AlignLeft | Qt.AlignTop
            Layout.fillWidth: true

            clip: true
            ScrollBar.horizontal.policy: ScrollBar.AlwaysOff
            ScrollBar.vertical.policy: ScrollBar.AlwaysOn

            ColumnLayout {
                id: listLayout
                objectName: "listLayout"
                anchors.top: parent.top

                Button {
                    width: window.width
                    Layout.fillWidth: true
                    text: "lsdjkfkl"
                    Layout.alignment: Qt.AlignHCenter | Qt.AlignVCenter

                }
                Button {
                    text: "lkdfjljfuiheff"

                    Layout.alignment: Qt.AlignHCenter | Qt.AlignVCenter
                }
                Button{}
                Button{}
            }
        }
    }
}

The thing is that I have my window, in that a simple row layout that has 3 elements in it :
left menu, separator, scrollview.
Nothing is fixed size because I want the user to be able to make the windows bigger if needed and the elements to adapt to it.
But because of my window doesn't have a fixed size you are telling me that the scrollview will never clip ?

The best way to present your problem is to give us a complete but minimal example that we can run ourselves. If you leave out essential parts, we're left guessing what else might be there, and we might even misunderstand the whole problem and basically answer to a wrong question. :)

So this is at the start

and if I add a lot of elements

you can see that the scrollview got bigger and it even pushed the window.

import QtQuick 2.9
import QtQuick.Layouts 1.2
import QtQuick.Controls 2.2

ApplicationWindow {
    id: window
    width: 360
    height: 360
    visible: true

    ScrollView {
        id: scrollview
        anchors.fill: parent
        anchors.margins: 60

        ScrollBar.vertical.policy: ScrollBar.AlwaysOn
        ScrollBar.vertical.visible: ScrollBar.vertical.size < 1

        ScrollBar.horizontal.policy: ScrollBar.AlwaysOn
        ScrollBar.horizontal.visible: ScrollBar.horizontal.size < 1

        clip: true
        padding: 1

        ColumnLayout {
            spacing: 20
            width: Math.max(implicitWidth, scrollview.availableWidth)
            Repeater {
                model: 5
                RowLayout {
                    // setting Layout.fillWidth for the RowLayout is technically unnecessary,
                    // because layouts have it on by default, but for the sake of clarity,
                    // if you use anything else than a layout
                    Layout.fillWidth: true

                    // set Layout.fillWidth for the elements inside the RowLayout to make them expand
                    Button { text: "Foo"; Layout.fillWidth: true }
                    Button { text: "Bar"; Layout.fillWidth: true }
                    Button { text: "Baz"; Layout.fillWidth: true }
                }
            }
        }
    }

    Rectangle {
        border.color: "red"
        color: "transparent"
        anchors.fill: scrollview
        opacity: 0.1
    }
}

here is the start

When I add elements the scrollview gets bigger and do not clip

Then as you can see if I make the windows larger it doesn't change the elements

import QtQuick 2.9
import QtQuick.Layouts 1.2
import QtQuick.Controls 2.2

ApplicationWindow {
    id: window
    width: 360
    height: 360
    visible: true

    ScrollView {
        id: scrollview
        anchors.fill: parent

        ScrollBar.vertical.policy: ScrollBar.AlwaysOn
        ScrollBar.vertical.visible: ScrollBar.vertical.size < 1

        ScrollBar.horizontal.policy: ScrollBar.AlwaysOn
        ScrollBar.horizontal.visible: ScrollBar.horizontal.size < 1

        ColumnLayout {
            spacing: 20
            width: Math.max(implicitWidth, scrollview.width)
            Repeater {
                model: 20
                Label {
                    text: "Something very very very loooooooong"
                    Layout.fillWidth: true
                }
            }
        }
    }
}

ScrollView {
 ColumnLayout {
    Layout.fillHeight: true
    Layout.fillWidth: true

because the ColumnLayout isn't inside a Layout. Try anchors.fill: parent instead.