Oh. I think I know what's happening. For this project I used the Portals 3D Plugin by Vojtech Struhar. The plugin works fine, but it doesn't transfer velocity when portal orientations don't match, and it is sometimes pretty buggy. If these issues happened in any of the following places:
The final door of the faucility before the evacuation complete text
The exit to the saloon in the dust city
The entrance to the sewers in the dust city (Labled "Dustys")
The halfway point of the green halls post-sewer
The exit of the green halls to the Alleyway in the Dust City
The transition between any two areas in the Upper Layer (To a lesser extent because this level's portals were mildly adjusted after I figured out the velocity issue)
Then you may have had issue with the plugin, of which I am unfortunately not smart enough to edit or fix. Otherwise, it may be an issue with the way doors work (Loading and unloading certain areas when given the que to) or with specifc parts of level geometry.