The quick colour picker (ctrl+leftclick while using Freehand Brush Tool), picks colour from a refernce image even if Show Reference Images is off, so that the reference images are invisible. 

Problem: This makes it impossible to pick a colour from any other layer, if there is a reference image at the location of the intended colour pick location and can be confusing if one is unaware that there is an invisible reference image getting in the way.

Additional problem: This behaviour is inconsistent with the regular Colour Selector Tool. When using that tool, reference images are ignored whether they are visible or not. (This behaviour is also incorrect: see bug 396144 https://bugs.kde.org/show_bug.cgi?id=396144 )

Steps to reproduce:
1 create new document
2 drag an image onto canvas and select Insert as Reference Image
3 make sure the reference image overlaps at least a portion of the paintable canvas (as it is possible to have it completely besides the canvas). If needed, use Reference Images Tool to move it.
4 turn off Show Reference Images in View menu
5 select the Freehand Brush Tool (B) and move it to the area of the canvas where the invisible reference image is located.
6 select colour by pressing ctrl + leftmouseclick

result: colour of reference image will be selected instead of colour of paint layers.

Expected result: colour of paint layers should be selected, unless reference image is visible. (If reference is visible it makes perfect sense to select the colour of the reference image.)
 
Have not tried in newer builds of Krita. (I am currently working towards a deadline, so am not at this time willing to risk messing anything up with the setup by installing/uninstalling)