Grongax: Thanks for the help! All of the scenarios seemed to be normal, and I didn't encounter any bugs, besides the one we're talking about now. Nimdok did not die in my scenario, but he did tell the Golem to kill the Lost Tribe.
Actually I think that helps a lot.
I believe I've found where the bug originates, and it's in Nimdok's scenario.
I guess this is spoiler territory for anyone not wishing to find out about critical actions that are accounted by the game for this scenario.
So spoiler:
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As far as I can tell, the game considers at least two actions as major during this scenario, and tracks them with global flags (this is separate than the "score" for Nimdok where I think more actions count). One is getting the mirror and looking at it, and the other is how you deal with the final choice about the lost tribe (when you have the Golem with you).
If you look at the mirror, then no matter what you choose in the final choice (kill the tribe or transfer control of Gollem to tribe) the game will consider the scenario finished.
However, if you don't take the mirror (or if you don't look at it), then the final choice can only be to destroy the lost tribe (or transfer Gollem's control to Mengele who will destroy the lost tribe, if you didn't have him look at the mirror). In this case the game will consider the scenario unfinished, and at the same time finished. Nimdok won't appear in the character selection screen, but AM's "epilogue" for the scenario suggests that Nimdok has to restart his scenario. Also, while only Ted is shown (if he is the last character), AM will not be using his special speech for the "final" player.
I will update the ticket on the bug tracker with this info.