Why can’t I sleep in houses that i own & why does taking things from them count as stealing

This happened to my wife, Aela the Huntress, when I got married.

What I found out, is that she teleported outside Riften's walls, and then began a slow walk back towards Jorvaskyr. (I could track her location because "Ask the leaders of the Companions about Work" was in my questlog).

Perplexingly, when I fast-traveled back to whiterun, I saw Vilkas and Farkas (who were both at the wedding) but no Aela. For whatever reason, she was traveling more slowly than any of us.

What this boils down to is that your newly wed wife is going back to her default location - so you were right to check the pub where you originally hired her - but wives tend to go about this extremely slowly.

My suggestion? Wait a few in-game days and then check the pub again.

So it actually seems to be not "unique", since it was encountered at least once in the exact same configuration by someone here. As in my case, there was the same combination of mammoth + dragon attack.

The elder scrolls wikia also mentions the bug of Skjor coming back, dead and clipping through objects.

Companions were also seen wandering far from their place here and here.

So my guess is: it might be implemented in the game that Companions go at random places in Skyrim to hunt big hunts (after all, they are supposed to be the mightiest warriors). Maybe it is triggered by becoming a Harbinger, maybe not (would need other conclusive proof).

Skjör seems to come back often, it might have happened in my game without me realizing. It seems to happen to Kodlak too from time to time. Being close, Njada followed and helped them too.

Both her and Skjör joining might be an effect of the CompanionFactionMinusBrillAndVignar faction. This faction thing could actually be the reason behind Skjör and Kodlak "resurrecting"

Edit: video of the bug happening: here and one with a variant here