The game designers didnt really get it that wrong when you look at what the pnp rule of frigfhtend is. Looking at the players handbook, it says that creatures who are frightend either flee from the source of fear as best they can, or if they are unable to flee they fight. They also have a -2 on all attack rolls, saving throws, skill checks, and ability checks when frightend. Your will save determines if you fight or flee, a sucsesfull save is a fight, a failed save is a flee. This fleeing action nwn puts you in is normal. The only thing they might have missed out is the -2 to rolls (who here has bothered to check if this happens or not? I havnt up until now). This isnt surprising though because the engine is not going to know if your charecter is in a situation to flee or not too, so logicly it makes you flee in all circumstances on the fail.
I suppose though if anything was to be done, they might be able to add in the -2 to all saves and rolls for X ammount of rounds/turns whatever, and then add in a second save to determine if you fight or flee. How possible this is I have no idea.