Not to mention if you're enemy to Civilian you can't open ammo boxes.

Checked it again, it's still borked.
You can try it out for yourselfs with this little snippet:

_sidearray = [blufor,opfor,independent,civilian];

{
_getenemies = [_x] call BIS_fnc_enemysides;
systemchat format ["Enemies of %1: %2",str _x,_getenemies];

}foreach _sidearray;

Then set the independent behavior in the advanced intel tab.
Indfor friendly to Blufor:
"Enemies of WEST: [EAST]"
"Enemies of EAST: [WEST,GUER]"
"Enemies of GUER: [EAST]"
"Enemies of CIV: [EAST]"

So far, so good, working as expected.
This is where things start getting weird.

Indfor friendly to Opfor:
"Enemies of WEST: [EAST,GUER]"
"Enemies of EAST: [WEST]"
"Enemies of GUER: [WEST]"
"Enemies of CIV: [WEST]"
How the heck are civilians hostile to WEST? Doesn't make any sense.
Shouldn't blufor be the good guys for civilians per definition?

Indfor friendly to Everyone:
"Enemies of WEST: [EAST]"
"Enemies of EAST: [WEST]"
"Enemies of GUER: []"
"Enemies of CIV: []"
Weirdly civilians are now somehow friendly to opfor.

Indfor friendly to Nobody:
"Enemies of WEST: [EAST,GUER]"
"Enemies of EAST: [WEST,GUER]"
"Enemies of GUER: [EAST,WEST]"
"Enemies of CIV: [EAST,WEST]"
Now all of a sudden civilians are hostile to both opfor and blufor but NOT to indfor, even if indfor is set as friendly to nobody.

This is making it extremely hard to have 3 hostile factions without having civilian faction acting weird to the good guys.

Does that make any sense to anyone?

I thought civilians flee when they see anyone with a weapon?

No, usually only when opfor is around.
So setting Indfor to either friendly to opfor or friendly to nobody will make civilians run away from blufor. Which shouldn't happen in any case at all, since blufor will never be a threat to civilians, according to the definition.

I think it should happen. Beacuse civilians should try to find cover from warfare like in real life, so if they see anybody with rifle, they should escape

This ticket is not about if civilians should flee or not, it is about the nonsensical state of side relations between civilians and blufor.