Holes/ missing layers (after retraction) in 3d printed objects
(answering my own question)

The problem was the extrusion distance settings in Cura's advanced tab, reducing the value to 1.5mm solved the problem.

Other problems with the same symptoms:


Partially blocked hotend nozzle.
Incorrectly configured steps per mm for the extruder motor - this youtube video shows how to test and configure this.