The post below contains spoilers for Act II and Act III.
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Issue in Act II
After reporting Matilda's relationship with a certain Brother to the archdeacon in Act I, every time I try to talk to Matilda in Act II, Andreas' and her speech bubbles do not show and I am stuck (the game does not freeze, though). I have to exit to the main menu and load my last save to continue playing.
Issue in Act III
The bug gets worse. I cannot anymore see Matilda's character anywhere, even though the scene implies she has to be there. Comparing with a friend's progress, she should be usually in the Town Common area and I only see the Brother there.
Below is an example (Christmas Eve scene/cookie cutting scene). All of Matilda's lines are marked as Magda's.