Ok, I have actually had this issue REAPPEAR in game twice again! At level 30, during the quest, A Night to Remember, I got attacked by bears, sabre cats, and pit wolves as normal during the trip to Morvunskar, then upon leaving all "natural" wildlife would run up to me as if they were hostile, and then just sit there... sometimes they would growl, but would definitely not attack... not even a red dot on the compass.
Interestingly, I didn't real the problem until a few unrelated quests later, and I just went back through my save files, loading the most recent untested save and running outside to see what the wildlife did. Unfortunately I didn't have a save inside Movunskar or the Misty Grove, but I did have one very shortly after the game teleports you out of the Misty Grove to the starting Inn, and the bug was there; but the bug was not present in the save right outside of Morvunskar.
So I picked it up again from there. I tried doing everything the same, taking it one step at time, saving and running outside, seeing how the wildlife reacts, and then reloading my save to proceed. Unfortunately, I did everything the same and could NOT reproduce the bug. To make matters worse, after playing again without issue for quite awhile, I noticed the bug again when I noticed the spiders in Skuldafn (during the Main Quest, the dungeon immediately after Odahviing) just sat there refusing to attack me. I should have reloaded then, but I honestly didn't think it would affect spiders, so I assumed that it was different bug. Then, after returning to Skyrim, I noticed that the wolves, sabre cats, and bears just sit there. For spoiler reasons, I just can't reload; it took me way too long to get through it just to reload and do it again.
I do really want to fix this. Granted I am sick of animals jumping me on my travels, but the materials from their pelts is essential for raising my crafting skill. It is actually really hard to get the materials without them being hostile. I have a theory that the game uses a command to "turn off" natural creature hostility during certain periods within quests like Misty Grove or when fighting Odahviing, and for some reason, with my mod configuration described above, it fails to turn on occasionally. Anybody have any ideas of console command I could try?
It is just so frustrating because the bug persists despite loading the save in vanilla Skyrim (of course I don't save when testing) so the binary method doesn't work. Any advice is appreciated...