My first though ...

Optimizing a design for manufacturing and fabrication should be part of your design process.
I'm pretty certain you wouldn't ignore the mechanical requirements of an enclosure your design needs to fit into, why would you ignore manufacturing or fabrication? Designing a product that is difficult and therefore expensive to fabricate, manufacture, or test is a huge mistake.

Always contact your CM to determine their manufacturing requirements during initial design. 

Also ..

You should have control dimensions on the drawings you are providing to your CM. If you have ignored the CM's requirements and the CM needs to panelize / repanelize the design for manufacture they must meet the specifications on your drawing. If not possible the CM must communicate to you that a design change is required to make the product manufacturable.

If you have provided dimensioned drawings and your CM is ignoring them it's time to find another CM.

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