You're probably a victim of the arrow gremlin. You see, there are wars going on in the Gremlin realm of Grendom. They run short of things like arrows, bandages, and other things. They send out scouts to pilfer those things from players. Sounds like you've been pilfered... ^_^
All kidding aside, you probably need to check to see if you accidentally dragged the arrows out of your quiver, but more likely you accidentally sold them back to a vendor when you were trying to buy more. If you right click on existing ammo in a quiver/pouch while the vendor is selling you more, they will happily buy back your ammo at a fraction of what they just sold it to you for. It's a great profit scheme and you need to be careful not to fall victim to it.
Just watch what you are clicking on when ammo-ing up. You'll probably never lose another stack. Don't work with ammo out of any kind of storage sack unless it's ammo meant for a particular target type. That will make sure it's not used in vain.