That's one way to look at it. Another possibility is that the item's magic only works for items of the right size. The unseen servants who live in the javelin slot have javelin-sized hands, and they're too stupid to realize that the smaller arrows slip through their grasp.Kershek said:The depth of a slot in a magic item shouldn't make any difference, especially in an item where you just think of the arrow you want and it appears in your hand.
Yet another option is that the quiver tries to be too smart. When you try to put arrows in the javelin slot, the quiver thinks you've made a mistake, and helpfully tries to shunt them into the arrow slow. But when it finds that compartment full, the extra arrows get spit out. (Hilarious "Ptui!" sound effects are optional.

There's no single, obvious 'right' way to handle it, so it comes back to DM call.