Why is my 3D printer doing this?

Hi guys,

I own an Ender 3 v2 printer and have recently bought one of the Eclipson airplane models to print on it. I am printing with LW-PLA and have been experimenting with the print settings to optimize the print quality. I don't have great experience in slicer terminology so this has been a bit of a struggle. The original gcodes for the plane which come with it don't print enough filament out (I think its not enough flow). This results in the walls of the print being very delicate and see through. I have since increased the flow and now have it in the right amount. Unfortunately for some reason the printer is causing the two holes on the bottom of the model to be disformed. I need them to be circular as they are where the carbon fiber rod will go. Below is a photo of the normal print vs the one with the issue. Note that both models look the same in the slicer preview, the holes are circular in the preview of the one with the issue.

Attachment 19482

Thanks for any advice!
Caleb