also check you haven't selected a fit to page/width/height setting some were
Yep, that was my first thought too
But, looking at the photo, I don't think it's that - typically the result would be bigger (and, for most PCBs, much bigger). I wonder if it could be a grid issue, perhaps the holes being laid on a 2.5mm grid. Placing the holes manually would be tricky if snap-to-grid is enabled and a slightly wrong size used.
@abdallah kishk - I wonder if posting your project (or creating one that demonstrates the problem that you can post) might help. I'm on 8.6 so might not be able to open it, but someone else might. That would determine if it's the project or printer that's at issue.