Posting the gerber files might clarify the problem.
We have insufficient information yet. If the PCB is made with correct component definitions and design rules, no short should ever happen. The PCB tool will automatically isolate components from copper pour.
But if your processor has e.g. an exposed pad that isn't correctly described in the component definition, anything may happen.
There are also specific trapdoors of some CAD tools, e.g. if copper pours are not automatically recalculated during the post process.