Depending what stage of the game you are at, could also be a skeleton archer, or Draugr archer shooting at the pen, hell even a grey dwarf throwing a rock, and the boar reacted (frightened) from the projectile hitting the wall, causing it to go crazy, but the other boar was out of range of the area effect of the projectile?

Also could be a nearby beehive you have built that is attacking the boars? I have seen that happen before on my old world, it happens sometimes.

A nearby enemy spawn could also be making them aggro, if there are no spawn preventing items near their pen.

Only other reason they won't calm down is a nearby fire.

Also stake wall is fine to use for a pen, I have mine in a stake wall fence & they breed no problem, away from fire, dark area, enclosed, protected by 2 star wolves 24/7 that kill anything that gets too close.