Serious bugs in the game

[Caelean]

I'm playing this game together with a friend. We play it together while talking to each other on Skype.

After the prison blocks we started to notice that our games started to differ. Small things at first like she gets growling and I didn't.
Then in the cistern she got a water monster and some red stuff while my game didn't show any of those.

Later in the Nave at the well where you're supposed to lower the meat in, there is no rope showed in my game and any interaction with the well and the meat results in "the rope must be raised to attach something to it".
Cranking the crank doesn't change anything.

After some trying we left the well alone and continued.

In the choir entrance, after interacting with everything, she sees dear bodies hanging from the ceiling but my hallway is empty and desolate.

Later when we woke up in the cell area, we walked into the half caved in cell and triggered the cut scene.
She sees a dead man and is able to reach the bucket in the cell next to it.
I can't see any dead man and I can't interact with the door to reach the bucket. We also notice that in my game the rope is missing in the well.

Anyone come across these or similar bugs? Or knows how to fix it?