I think it depends on how specific or detailed your style guide is. If you have tried to read either the Windows or Apple style or UX guide, you'll find that they are designed to provide general principles on how to design the interface and interaction, but are far from perfect. In fact, often the confusion is generated from people not interpreting the style guide correctly, or applying it in situations not explicitly covered by the guide.
One of the most common scenario that I come across in interface design is when the style guide has been tailored to the product or software application and then the requirements change so that a conflict arises (e.g. trying to use an interface component to provide a function or feature for which it is not designed for, or creating a custom component/control). I don't think you should expect that the style guide will stay the same, but hopefully the design principles that you base the style guide on is not so generic or specific that it will cause conflicts in the decision making process.
As far as handling exceptions, I think the best way to handle it is to highlight the conflict to the aspects of the design principles and style guide by outlining all the potential changes and impact to the product or software application. Also, it depends on whether the style guide is used to define the product or if the product is used to define the style guide, and how the design/sign off process works within your particular organization. UX design processes should serve the purpose of the organization and not the other way around, so you need to be able to adapt and accommodate these changes in the best way possible.