The following example demonstrates the issue:

import QtQuick 2.0

Rectangle {
    width: 400
    height: 400
    color: "black"

    focus: true
    Keys.onReturnPressed: console.log("return pressed")
    Keys.onEnterPressed: console.log("enter pressed")
}

Running directly in Windows, using the main enter key of a keyboard outputs "return pressed", and using the numpad enter key outputs "enter pressed". Running in webgl both output "enter pressed".