I have been having this issue lately where when I re-size a group of shapes (like a grid of boxes) - when I scale down the composition by using the Transform Tool - Those same boxes in a grid will not line up as they would in the original size. When I scale back up to the original size those boxes in the grid will now be aligned incorrectly like the original version of the illustration. Also, my strokes are now thicker when I re-size back to the original artwork. I have an image attached that shows this problem pretty well.
Any ideas? I have been looking through my settings. I also shared my file with a colleague and he had the same problem with my file.
This is a super weird problem and I hope the community will have a solution?