Deformation in small scale breps

Hi, I’m trying to cut a series of surface with a sphere in order to get circles.
But at some scale the circles desapear or deform into other thing

The general idea is to 3D print a piece that conect a series of plastict pipes and also support sacrilic panels

I’ve saw a tutorial of glass panelling that I was trying to follow but can’t make it

https://www.youtube.com/watch?v=8RZk0e7WE38&t=545s

Thank you for your time