D&D 5e damage die rolled as Disadvantage

I turned on 3D dice and auto roll and noticed that when I roll an attack, the damage die is rolled as if it were a disadvantage giving me the lesser roll. The advantage toggle should only work for the d20, but if I set the toggle to Advantage, it actually takes the higher damage roll. Any idea why? Here's another example with a different character in a new game: Rapier : 1d8+5 Sneak Attack : 1d6

I think the other damage dice you are seeing are the critical strike damage rolls.  They are hidden in chat by css unless an attack roll is a crit.