DustyRhodes,
If your drawings are prepared perfectly, any non-conforming part will not work.
The idea here is that the part does not conform, but it is good enough. This reflects bad design and drafting, a bad attitude by production, and/or poor manufacturing quality. Someone's crappy work and bad methods have been validated, and you will be seeing more of it.
I do not think there is a standard process here. You need to look at all your practises before production and vendors get to assume that all of your tolerances are negociable. Perhaps you are producing bad drawings. Perhaps some of your tolerances are unfabricatable. Perhaps production is unwilling to upgrade or repair bad equipment, or perhaps someone in production is an idiot.
As a designer, I want all my tolerances met. If there is a problem, I want production to come back and talk to me so that we can sort things out. Maybe I am too accurate for the process, and I have to redesign to allow for looser manufacturing. Perhaps they have to try harder, or use a more expensive process.
There was a article out a couple of years ago stating that the Japanese fabricate cars to sloppy tolerances, and they provide spacers and stuff to production. The article described this as an example of Japanese cleverness. My interpretation was that the designers understood the capabilities of their fabricators, and designed their cars to be assemblable under those conditions.
JHG