Kalcifer

Could you explain why the discrepancy is there (is it a legacy issue or there for mathematical reasons for example)?

Is this is a bug or also true of physical Lego? Using version 4.3.8 on Mac OSX 10.10.1 The holes that pass through the side of Technic bricks are misaligned slightly higher than they should be, which causes an array of problems. Red brick (87087): Blue brick (6541): Green bricks (3023): To reproduce the bug take a 1x1 Technic brick (a 1x1 brick with a hole that passes through the side) and a non-Technic ('normal') 1x1 brick with a knob/stud on the side, attach the vertical knob/stud of the normal brick to the vertical hole of the Technic brick and you should immediately notice that normal brick is very slightly higher than the technic brick, this is the same when the normal brick is rotated 90°. This bug can be replicated with two Technic bricks and a connector peg with a knob/stud (4272), however the misalignment is only apparent when one of the bricks is rotated 90°.