I dont know is it a real bug but i know its strange.
So if you have 1 piece of dye in your hand and you painted the collar it seems you still have the dye BUT if you want to put it into a stack it disappears. BUT if you leave it alone you can paint another collar with the same dye. (( so you can paint twice with the same dye if you didnt put it into a stack)) BUT if you use a stack of dye if you paint a dog collar it removes one dye from the stack.
I know its not the best description but its hard for me to describe.
You should try it and you will see. ( Dye a dog collar with one piece of dye, and try to put that dye into a stack, and try to dye a collar with a stack of dye).
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It seems that the ItemStack is reduced to 0 but not actually removed, causing the item to become phantom. It can be dropped on the ground, repeatedly, and you will not be able to pick it up again because it is 0 items. I can't get rid of this phantom ink sack. If you try to put it in a chest, it duplicates instead.
Edit: Phew, it seems the phantom ink sacks can be absorbed into stack of one or more ink sacks (by dropping them nearby) to remove them from the world, and then dropped normally after being absorbed into a stack to remove them from your inventory. Scary.
Confirmed. When dying a color with a single dye, that dye will not disappear. Moving this dye to a stack will cause it to be removed from your inventory. Dying while holding multiple dye properly removes one from the stack, however.