Flattening bit doesn't touch waste board

My board is the standard baseboard that was shipped with the Shapeoko 3 xxl and my spoil board is 3/4" MDF. I can fix this by adding another 3/4" board on the baseboard, then putting the spoil board on top. This is my first CNC, so I don’t have plans on working on anything with depth (like boxes or real thick stock). I just wanted to check to make sure it wasn’t user error.