Less than an hour in, it seems like my save is already bricked.

I'm in this room in the Necropolis where you have to take the block out of the wall, push it down to the floor, go across the room, flip it up the stairs on the other side, and then into a hole in the opposite wall, to open the lower gate.

The block is 1/4 off its normal grid, and I can't push it all the way into the wall. No idea how it got that way. Save/load has no effect. Is there any way to fix it?

I wasn't able to fix it, but I did find a workaround. Loading the game starts you back at the beginning area. So I ran back to this puzzle, jumped onto the scale to raise the other one, and then saved and quit. Loaded the game again, went back to this room again, and was able to jump across without ever opening the lower gate.

That workaround probably won't work next time...