That is strange. Duty shouldn't be actively hostile at this stage unless you attempt to pass through the gate without their permission. When you took the documents from the Agroprom military base, Barkeep should have warned them that you were coming, so that shouldn't be a problem.
When you approached the Duty outpost, did you get the task to help kill the Boars? I am not sure, but I think you need to do this even if the gate has already been opened. It is also possible that someone was hit by a stray bullet and they blame you.
If you have done the necessary tasks and they are still hostile, try using the Attitude menu (ESC+F) to change their faction attitude to neutral. From memory I think you need to enter dolg for Duty faction.