This is certainly not a new issue...everyone has had this happen to them at one time or another while missioning. It's a pain, no doubt, but there are a couple of preventative measures that might help lessen the frequency of this occuring.
First, try not to have people leave the mission area...this can be tough at times because, as you said, sometimes a group can get overwhelmed and need to escape to prevent death. However, if you can, have group members retreat to the area just near the elevator, which should be cleared of NPCs by the time you start making your way through the mission area. If a player is escaping a particular NPC or group of NPCs, try to focus fire on that single or group of NPCs to help the player make a clean escape to the entrance area I described. Again, this isn't a fool-proof safety zone for the players, but it's better than the elevator as far as NPCs being able to escape the mission area is concerned.
Second, try looking for missing NPCs near the 'origin' point (0, 1, 0 on the map coordinates) if you are doing missions in the Richland/Westview area. Sometimes (mind you, not ALL times) NPCs 'retreat' to this area after leaving a mission area in the Richland/Westview area. Again, this is only limited to the Richland/Westview area and isn't fool-proof, but it's a shot.
Thirdly, if in a group, you could ask someone be posted near the elevator to help catch any 'escaping' NPC's before they get too far. This way you may catch them before they disappear outside.
These are just some suggestions I thought may help, but again they may not work in all cases. This is just one of those many 'fun' bugs we have to deal with when it comes to missions, sadly. Hope this helps!
