No they don't remain after fast traveling(thank god) aside from being "stuck" when you save the encounter theres nothing really wrong.
This is what i mean

http://cloud.steampowered.com/ugc/541797441533152894/420DBD4CDE308D3DD7BBCE727C6CD35586F096E1/
The stormcloak prisoner simply "refuses" to move >.< regardless of how long you wait.
And No i have NO mods installed! and yes i've verified integrity of game cache