As soon as I try to start the Animal Extermination quest line, Aela will stop treating Breezehome as her home and will stop her AI packages she's been using. Anyone have any idea what's going on there?

Is the Animal Extermination related to Aela or the Companions and their quests in any way? I haven't done any of those quests yet, but if they interact with each other, it's likely that it's a bug that someone may have patched with a mod.

The quests she gives you and marriage are completely separate, and never shall they intertwine.

It's a companion quest that you get from her. As soon as she gives it to me she stops with her current AI package, goes to Jorrvaskr, and never goes back to Breezehome.

I think the wiki mentions problems concerning this, because I looked into it before marrying her. It may mess up her totem quests too.

If it helps, I did all of her quests and then married her after collecting all the totems, and so far everything is fine.

I was able to do the totem quests without incident. The only thing that is acting weird is the Animal Extermination quest.