Well, this wasn't the cause behind ALL of the problems, but, during the era of Oblivion, Fallout 3, and NV DLC, both Bethesda and Obsidian went on record several times as stating DLC can neither be patched, nor can DLC interact with DLC.
If a DLC adds a perk that makes all X class of weapons get 25% more damage, the only weapons that perk can effect are the weapons from the base game, and THAT specific DLC. If a DLC released before or after it added X class weapons as well, then the perk couldn't effect it, because it came from another DLC, and DLC can't interact with DLC.
This is also the reason why the home added in the Dragonborn DLC, which released after Hearthfire, lacked any and all of the Hearthfire home improvements, since they came from different DLC.
I am not 100% sure why they can't, but I think I read somewhere it has to do with doing so making DLC dependent on each other, forcing people to buy every DLC, or just have none of the DLC work at all. That or they would have to release a weird series of mini-mods, that basically server as compatibility patches between the various DLC, which would be difficult to keep track of.
The rules were, from what I remember
-DLC cannot interact with the base game(You can't tell Caesar you killed Ulysses or Graham for example)
-DLC cannot interact with other DLC(You can't show Christine or Ulysses the tapes you found in OWB for example)
-DLC cannot be patched, which is why none of them ever were.
-The base game CAN interact with DLC(Such as telling Graham you killed Caesar, or telling Wernher you heard about the Pitt from Kodiak in The Citadel)