I was able to replicate the issue, and I determined what causes it (but not why).

Long story short: delete the keyframes.

More detailed explanation:
I tried retexturing the entire map, deleting all portals and detail brushes, making this wall detail, deleting all except that section of the map, moving the geometry of the map to a new .rfl file, remaking the geometry, making new portals (one of the portals in this map is REALLY broken), nothing seemed to work.

After a ton of testing, the only consistency I found was that the issue only happened when the shooter is aimed in a certain direction. It doesn't matter if the victim's hitboxes are within the collision mesh of the wall brush (as I originally had thought). This direction happens to be towards the white "walk-through" boxes in this map, which are movers set to "No Player Collide". When I deleted these keyframe objects (but not the brushes themselves) and rebuilt geometry, I was unable to reproduce the issue at either of the two locations your video showed.

I was also able to reproduce this issue in other areas on the original map. If the victim is standing between a mover brush and the shooter (regardless of other level geometry), he will be hurt.

I don't know of a way to fix this issue yet. I've tried a few different tests, but the issue is still present. For the time being, I think the only way you're going to avoid this issue is to remove those movers (the walk through white boxes).

I hope this solves your issue

So.. in other words , your going to get rid of some useless keyframes that glitched the map ? People wont notice this ,,wallhack'' since we're used to frag from our points of view (face-to-face) but not on the opposites of the walls.(when not having the Railgun)