Which slicer do you use?
We have also encountered problems with Slic3r-PE 1.41.0 printing round things.
https://shop.prusa3d.com/forum/hilfe-zu ... 24917.html
Try printing the Benchy with Cura and see if it looks similar, to be sure the issue results from your printer.
It can also be on your printers Z-axis, the spindles rotate eccentrically at a certain height, but...