Inaccurate inner size

Say, when printing a cylinder with a hole, the outer diameter will be within 0.05-0.1mm, but the inner diameter will be 0.4mm (nozzle diameter) lower than it is in the design.

Why is this happening?

Is there a way around this other than taking it into consideration in the design?

You can use the inner contour offset option if the z-contour is always an inner contour thru the hole

http://forum.zortrax.com/index.php?/topic/2581-different-diameter-in-a-same-holes-using-offsets-holes/?hl=offset#entry28520

Also, the hole diameter will change by 2*offset because the offset is on the contour, not the hole diameter.

Holes ending up smaller is common in 3D printing due to shrink (especially smaller holes). If you think there is another problem, it's helpful to upload stl and zcode.