Ancestral Spirits are designed to be somewhat friendly. It is possible for them to have a range of personalities, and I've heard of "wild ones" going rogue, but never beheading an entire party.
Did it use a weapon?
I will definitely take a closer look at this. Don't be shy to report anything else you may find.
It had a carving knife, if I remember correctly. That was the only time they'd ever actually killed my entire party, but there have been other times where they still attack. However, it's almost always in defense. Every time I've seen Clerics raise them (multiple worldgens, half a dozen characters with different Clerics in the party) the Clerics immediately start attacking them instead of treating them as neutral or allied. Clerics randomly trying to kill the Spirits seems to be the bigger issue, not vice-versa, which then causes the Spirits to go wild and start hitting everything around them.
Also, gotta say I rethought about it and I honestly think the Aboleths are just a touch too strong. I don't normally complain about tough monsters, but this "apocalyptic creature" very often gets large Hamlets (and even a town in my worldgen), and even one of them can easily kill a high-skilled combatant with full steel equipment, even with half of their body severed or cleaved open. If they didn't have Hamlets, I'd be fine with them being this tough, but it just seems silly. I have an easier time fighting Dragons than I do Aboleths.
Also experienced what may be a bug near hostile "Shadow" warriors and wrestlers and such. Me and my companions constantly lose consciousness, as do other NPCs around us, and in one instance I got near a Shadow Swordsman and suddenly had both my hips mangled beyond recognition. Nothing happened in the announcement log and he didn't attack me, I just got injured out of nowhere. This only happens to me around Shadows and I can't tell if it's intentional or an ability of theirs or just a bug.