Kicad-5 rc3 and rc2 debian has (I think) bug in pad clearance when gerbers are generated.
Square pads or square pads with rounded edges
are rendered with 0 clearance to the solder mask
in gerber files.
I tried to force pad-specific clearnce e.g. 0.1 mm.
it is correctly shown in PCB opengl view but it still
doesn’t appear at gerbers.
If the same pad is changed to oval or round shape,
then the clearance appears correctly in the gerbers.
Davor
KiCad’s internal clearance markers should not show up on the Gerbers.
My point is not that I need to see clearance markers
in the gerbers, but the SQUARE PAD size has identical
size as the SOLDER-STOP MASK while it shouldn’t be so,
solder mask is set to be larger by the CLEARANCE value
which is not honoured for SQUARE PADs.
Clearance value is honoured only for ROUND PADS or
OVAL PADS, in this case SOLDER-STOP MASK is
larager than the PAD as set by CLEARANCE value, correctly.
Don’t worry, the rest of us understand what you are talking about. 
You will need to report this on the bug tracker. See the FAQ on reporting bugs.
This does not seem to be a Gerber problem, but is a bug in Pcbnew calculating solder mask or maybe the plotting.
Gerber is just a photo plotting format and does not really know anything about layer types.
I have changed the category.
Please register the bug on Launchpad, ideally with a sample.
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