All containers empty in Story Quests

AAN2

So this has been happening since I purchased the game on Father's Day, but I figured it might be a character specific glitch or something. It's not though, two additional characters later and I still cannot find a single lootable container while doing a 'solo dungeon' story quest. Here's the specifics.

All Fighter's Guild Quests, Mages Guild Quests (with the exception of Eyevea), and Main Story quests that involve dungeons are effected.

All containers will appear properly, but will all be empty. They do not appear to be full and then turn out to be empty, they are just empty. Crates, urns, sacks, jugs, and even chests will appear to have been already looted.

Is this intentional or is it some weird glitch, and how can it be fixed?

AAN2

This has improved a bit, but over 75% of the containers are still empty. In solo dungeons with more than one area (where you have to go through a door, like the mission with the wabbajack) though, the containers are 100% empty. Solo dungeon enemies also rarely drop loot still.