Spoiler alert and bug report!
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I am playing on PC, with a new file starting from the beginning and doing Jin's route. When I presented the Scriviner badge to promise to protect him, the admiral and scriviner sprites got misplaced. This didn't happen to me before, even if I didn't play Jin's route in the older version. Idk if the other routes have the same problem in this version or if it's only Jin's route.
They stay like this through all Jin's testimony even, having Admiral's arm besides him through all of it.
EDIT: I know you said older files would have problems and you're right, I loaded a Leo run in this moment and it had the same issue, but in the 0.6.2 I didn't have that problem. Hope it is helpful and I'm excited already for the next update when it comes ^^