Don’t know what is the aluminum disk you are referring but normally the cnc table top is covered with a sacrificial material (MDF or anything similar available in your country). This sacrificial material means that you don’t care if it is damaged during the operation of the cnc and normally it is damaged and depending on the use, you replace it as needed.
Then use your cnc with an appropriate cutter to take of lets say 1/16" or 1/8" of the top. After you surface this board you leave it always there until the time needs replacement.
I can't say if there is something wrong with your machine but I will check all points to assure that there is nowhere any play and everything is tight and smooth.