Multiple designs on a single PCB

I recently ordered a PCB for a design that consists of two boards stacked on top of each other. I put them on a single PCB with milled cut-outs to allow the to be separated. After ordering and paying I got a message that said I had to pay an extra $19 since my PCB contained more than one design. I often stack boards on to of each other to get a compact solution. Why is this considered multiple design?