cura shows different Z heights Cura v2.5.0
I've been working in Blender for some time, so I have experience with exporting stl from it with exact size and I had no scale issues with slicing.
But today cura showed a strange thing.
These are 3dBenchy and a stretched cube which are supposed to have 45mm height, also "boundary boxes" are turned on to show that there is no flying geometry.  

  

As you can see below cura shows same size visually but different in numbers.
  

And if I scale the ship inside the cura it will look like this
(low reputation) http://dl3.joxi.net/drive/2017/08/01/0001/2747/88763/63/969fe8bc67.jpg

Does anyone know if I screwed up the model somehow or can it be considered as a bug?
Converted comment on OP to answer:

The comment links to a question on SE.Blender; the answer that led to the solution is quoted below.


  The STL exporter doesn't take Scene Scale into account. Import your
  STL back into Blender (it will have the same size) and drag Scene
  Scale up back to 1.0, and you'll see how the cube grows relative to
  the grid.
  
  1 Blender unit equals 1m, but STL seems to assume 1 unit as 1cm.
  
  If you want 1 unit to be 1mm, set Scale on STL export to 0.1 and 
  Scene Scale to 0.001 to make it match the output scale in viewport.
  
  Note that the STL will be 10x smaller if you re-import it into
  Blender!