Apparently related to the Bastian Hallix companion perk? Most of the time the bottles give you nothing instead of a potion or a reagent; this has been theorized to be related to if you don't have him/his perk active when looting them, in short it rolling against his "upgraded potions" check at all times, but if you don't have him/his perk, then you end up looting nothing. I don't know if the theory is sound, but I can definitely confirm looting a large number of alchemy bottles, both stealing and non-stealing, and no matter what it's a constant empty bottle experience. Maybe it's locational? If so, it was on Stros M'kai and Betnikh that I experienced it the most, but there was also some in Daggerfall that I looted that I still experienced this, so I don't think it's locational.
In short: Alchemy bottles bugged, not giving potion/poison/reagent loot they're supposed to, theory is that the wrong loot table is being called by default resulting in nothing looted for someone who doesn't have the appropriate perk to access said loot table.