So I just got all the brass wedges and put them in the safe in the cellar of the church and... the door just opened. I was obviously expecting a puzzle, so I looked at a walkthrough and sure enough there's meant to be a puzzle there.

Similarly, the safe in the cellar of Hamilton's cabin just opened with no input needed. I'm mostly playing this for the puzzles so, needless to say this is a bit annoying.

To anyone else who played the GOG version, did those puzzles work for you?

Strangely the walkthrough posted on Steam details the safe puzzle, so it must have worked for someone at some point.

Randomly occurring or a bug which wormed into the "latest" version maybe.

I guess, yeah. I wrote to Artifex Mundi to report the bug. Not so much that I plan to replay the game, but just to make sure they know about it. Maybe they'll fix it?