If I put 2 Spears on a character sheet, I get two identical entries with a quantity of -

This actually seems to apply to all thrown weapons (except dart) with a range of 20/60 or lower, such as hand axe, light hammer, etc.

If I put 20 javelins in my character sheet, I get a single entry with quantity 20

As javelins are also melee weapons, I don't understand why there is a distinction as to why they are stackable and the other items are not

Hmm, might have to do with what are designed to be bought in bulk as thrown weapons and what are meant to be melee weapons that happen to be throwable.

For example, 5 javelins can be starting equipment and javelins can be stored in quivers. And 10 darts can be starting equipment. I'm going with bulk starting equipment as the deciding factor.

Outside of bulk starting equipment possibilities:

The only mechanical differences between javelins, and spears

Javelins weigh 2 pounds, have a range of 30/120, and and cost 5s
Spears are versatile, weigh 3 pounds, have a range of 20/60, and cost 1gp

Bulk starting equipment is probably the deciding factor, but I'm still going to chalk this one up as a defect, because it is reasonable for a player to want to have bulk throwing weapons besides javelins / darts
Darts are actually explicitly ranged weapons

This defect applies to
Dagger
Hand Axes
Light Hammer
Spear
Trident

All of which are thrown, but not stackable

This came up, when I took my polearm master character, and tried adding 20 spears (The character is a centaur, so carrying 20 spears isn't really a big deal, with some side bags)

Maybe just use custom items for it. They stack.

I tried a custom spear, and it still isn't stackable. 

Custom Javelin doesn't work, because the range is wrong, and range isn't something I can select for throwing weapons

Let me elaborate. On character sheet in equipment, manage equipment, under custom items click create custom item, rename it "extra spears" or whatever you need, give it the weight of a spear (or whatever), and add an amount equal to the number you have -1. Add 1 of the item you have multiples of to your sheet for the stats and treat the "extras" like an ammo count, ticking it down when you throw one.

Thank you for the explanation

Seems like a reasonable workaround

I'll do that. 

Seems odd to me that some items are stackable, and others are not

You'd think all items should be stackable, since it would allow items to be standardized, but alas

Thank you for the help!

That method appears to have worked. It's not perfect, but it's good enough for my uses! Thanks!

If all weapons stacked, you wouldn't be able to dual wield.