Different squads have different ammo available in the military screen. There is no apparent reason for this.

Marksdwarves are not able to select the majority of the bolts. Coincidentally the majority of the bolts are in two bins in an ammo stockpile. Newly made bolts that are not stored are picked up by marksdwarves and stockpiled in non-bit stockpiles properly. Dwarves do not seem to want to take bolts out of the bins, regardless of waht you do to the stockpile settings. After some creative dumping I was able to empty and restockpile many of the previously binned bolts. So far however it seems like bolts that are re-stockpiled do not show up on the ammunition menu. Dwarves seem to only pick up newly made bolts.