You are apparently trying to make a mixed plane/signal layer with additional "positive" traces. The pdf seems to show only the negative part of the plane.
The question is, what's your CAD tool and how does it support gerber generation for mixed layers. We can't know.
It's often easier to make mixed layers as positive (signal) layers with a copper pour filling the free space.
With "increased board size" you probably mean the copper outside the board outline. That's normal for negative gerber files, you don't heve to worry about it.