3D printing, while very different from injection molded parts, still requires knowing what to do based on experience from having done it (whatever ‘it’ is).
Not all features are in contact with the bed, there is asymmetric environment heating, cooling fan, what you use to hold parts to the bed… not to mention different filaments... Internal stress/strain, asymmetric annealing from sitting on bed...
If your holes are the only issue, then change the diam accordingly to produce the desired result.
0.42mm is the thickness of 4 human hairs - how accurate do you need the holes in a prototype?
Are the holes on the bottom layer (on the bed) where the material gets smooshed out into a Brim?… Are you measuring the brim?
This week I designed a thing with small holes; the goal diam = 2.0mm, the printed result is 1.95mm (the difference of 0.05mm is one-half the thickness of one hair). To get that result, the model uses 2.2mm diam.
Note, I measured with calipers, thus some inaccuracies due to the flats as opposed to using a measuring dowel. If I used a dowel, the actual would probably be ~2.05mm and I did not punch-out the minuscule brim.
And, that’s on machines built from low-cost kits!
3D Print Parts