you have an old version of SketchUcam(?)
and
you have a line intersecting the hole.
the little colored line that designates the hole position must not have anything crossing it.

but now, I must ask if you are using the latest version of SketchUcam? V1.4 is what you want.
I ask because since a few versions back plunge holes get grouped during creation and this solves intersection problems excepting for overlaid horizontal lines which will just prevent the plunge hole being cut at all.

quoted from the help

if you really have to drill holes on top of an existing line, group the underlying line before adding the plunge holes.

 

yes, I normally draw a triangle toward the lower left, so the hole center is the top right corner of the triangle.
this way the plunge hole never gets interfered with, and can be deleted and replaced without losing the center.

cross hairs will work, so long as no part of it is horizontal, or if it is, group it before placing the plunge hole.

if you are putting a plunge hole inside a drawn circle of the same size, you can get an intersection at the end of the colored line, and hence 2 holes drilled. remove the drawn circle, replacing it with either a center point (there is a plugin for 'set center point' that will do this for you before you delete the circle) or a triangle that indicates the hole center (smaller than the bit diameter!)