Clicks within the advanced build mode menu, will also register as building/removing on the ship that's behind it.
If you expand the advanced build mode menu enough, you'll get a scrollbar and clicking on the scrollbar will enable "paint" mode.
The paint mode is something that auto placed blocks where you're looking at (only works in advanced build mode) and it only does that on a certain plane set on where you triggered it, at least with this scrollbar thing since I have no idea how to enable this mode manually.
You disable it with double left click though (in advanced build mode)...
UPDATE:
Also happens if you use sliders, seems this thing is used in SegmentBuildController, variable: timeButtonPressed and MULTIPLACE_DELAY
timeButtonPressed doesn't get set to 0 when needed, resulting in this behavior.