This happens, almost literally, about 1/30 times I transition and I only just realized recently that it isn't supposed to happen. It's happened one in Foothills and once in Wyldewaters (I can't remember which transition it was, but both times it put me right in the middle of dangerous mobs) and once when entering the Shade quest area initially. The PC I was using was Haroth Ravenwind on the account Haromaro, if that makes any difference whatsoever.
This is a bioware bug, as far as I'm aware.
The two times i've done the Black Canyon Quest, this has happened to someone in our party. It may just be bad luck due to the bioware bug but perhaps there is something wrong with the transition that is making it happen more often?
I believe this happens on EFU more often than other servers due to the fact that many transitions do not properly use waypoints. My own theory is that when a bit of lag occurs and a PC remains on a coordinate that is over a transition (for example, those that you often have to use the mouse to get out of rather than simply walk away) it loses their position on the x-y axis.
Hm! Switching it to a WP.
If this happens anywhere else, make a report and I'll switch to a WP.