Unfortunately, i did not get the alraune ending either. I don't even know how to get those endings yet as i have yet to get a single one. However i wouldn't be surprised if the ending is the cause behind the game getting confused.
Currently (Bad) Endings are just the defeat screen you get when losing with a lot of body parts for a certain tf. Basically you get a variation of the ending screen depending on the trasnformation you had. Nothing special yet. "Actual" endings are currently not implemented since the game cannot be beaten yet. But I am planning to have different endings depending on transformations in the full game.
Oh almost forgot they also only appear when losing because of corruption if I remember correctly. But since you haven't seen those you didn't get the Alraune Bad end which woud have triggered the achievment so it might be a bug.
I will try to replicate it when i have time and get to the bottom of this.
Thanks a lot for the reports!