Okay, so since I was quite worried (and maybe I should say obsessed) about this issue I started doing some tests, first to figure out where in the .level files the vertices were being stored, and then a few simple tests to determine the origin of this issue.
You may have noticed that sometimes you have slightly off-grid vertices in your maps (I remember seeing them in Summit and Tram, too, not sure if the authors have taken the time to fix them), causing micro-cracks, you can see them as little dots that let you see into the void.
It was suspected that it was caused by rotating or moving multiple objects (specially when the multiple selection has props, which makes the center go a little off), but I found out it actually happens with a single face being selected too.
First, the levels store the coordinates and distances in meters. But that didn't seem to be the issue, since when I switched to a metric grid the same issue happened. The test was very simple, I made a square, then proceeded to move it from the center and saved, then I cycled the movement origin to one of the vertices and moved it around and then back to the original place (to realign), when compared, it shows how the vertices go slightly offgrid when moving from the center (default).
It also happens with the rotate tool (no matter where you rotate from) and the scale tool all the time. See a few posts below to see another (different?) issue with the scale tool.
I actually wanted to make a tool to take the coordinates and if they were "off-grid" more than 0.0001 or something to re-align them, I almost found this by accident. You'd need to convert to inches and then back to metric (unless the map was done in a different grid, since they do not line up).