Why will I not always be able to fully reload my weapon?

Sometimes when I go to reload my weapon it won't be fully reloaded, and instead will only be partially refilled (i.e. I can only have 2-bullets in my Makarov even though it can hold up to 8). I originally thought this was just a bug, but it seems to happen quite a lot.

Why will I not always be able to fully reload my weapon?

This isn't a glitch, it's just how Arma 2's ammunition system works. The wiki contains more information:

Many FPS players are used to pool-type ammunition systems (e.g. in Left 4 Dead), which refill the current magazine directly out of an unsegregated pool of bullets. Arma 2 uses a more realistic magazine system. [...] You can only change magazines; you cannot refill them. When you reload, you place the fullest available magazine into the gun.

Try to fully expend your magazines if possible before reloading. Near-empty magazines still take up as much inventory slots as a full one, so mind your reloading. Let's say that you begin with a full Makarov PM (8 rounds) and two spare magazines. You shoot 4 rounds and reload. After the animation is complete, one full magazine is in the Makarov, while one full magazine and one half-full magazine are in your Inventory.