i have both versions of fallout 3 (normal uk and GOTY uk) and both show this strange behavior.
When i go directly from vault 101 (mostly swimming) to rivet city to get the bubblehead intelligence, i am encountering a problem.
On the way back, the streets are empty. No encounter or NPC apears.
Sometimes direct behind me a monster appears from one second to another.
It is not appearing in the distance, but directly in my neck.
I hope you now the issue and maybe there is a patch to fix it.
best regards
Fabio