I don’t know what you’re printing, but holes are normally not included in the copper for Gerber files.
The reason is that this is both not needed for a normal production process because the holes are normally drilled (and then plated) before etching.
For hobby use and hand-etching & drilling it is usefull to have small starter holes for centering your drill in the middle of pads & via’s. I think there is a setting for this during plotting of output files, but I’ve just now looked a bit at it and am not sure what setting it is.
There is a setting for “Drill marks” during plotting, but it’s disabled for gerbers.
There is also a difference between:
Pcbnew / File / Plot (Vector output)
Pcbnew / File / Print ( Pixel output (I think))
… And I see that also in the “Print” output dialog there is an option for “Drill marks”