I confirm Lazur's comment that a low value for caps exacerbates the issue (but no combination of parameters makes it disappear).

I've tried a few combinations and fill rule does not have any effect on these holes (which makes sense as they are in fact genuine errors in the path as I can check with the node tool, so rendering should not really matter), nor do any of the settings of the calligraphy tool.

The Calligraphy tool invariably produces paths with "holes"/"defects"/"artefacts" whenever the pointer moves slowly. http://i.imgur.com/JCnbLOd.png The black stroke on the left is with a mouse, no pressure sensitivity, the red strokes on the right are with a Wacom table...