I believe something like this is being worked on, although it may be a while before you notice any changes in game.
You can find the log file in the location %LOCALAPPDATA%\Turbulenz\Boundless\log.txt. If you are using Windows, then you should be able to find your username within the Users folder. Otherwise, the log file should have the username near the very top.
Thanks for the video, it clearly shows the issue in action, so I’ll add this to the existing bug report.
Your coordinates didn’t stop outside the exact portal, but the situation you have here would apply to any portals built in front of walls, where it would suddenly flip and place you in this predicament. If you do get the illegal protocol message again, be sure to share a game log just after it occurs.