More than once I was crushed to death by a door that opened inwards. A couple of times I would destroy a crate that was beneath a second crate and the crate on top would not fall to the floor, even though there was nothing supporting it. Usually the crates would fall, which indicates that this is obviously a bug. A few holes even sat the smallest fraction of an inch off of the surface they were supposed to be set into. These are problems with the engine itself which need to be resolved.
Levels are really long to load.
This could get a little frustrating. With the patch, loading saved games that occur on the level you've already loaded is rather speedy, and for that I am thankful. On a couple of levels where you had to walk through water, the water surface did not reach all the way to one wall. This gave a rather odd effect where there was water on one side of the hall, but not the other. In one room, I got stuck between a sloping wall and the ceiling.