I guess I can't really elaborate without spoilers, so other readers beware!
After the room with Roy, the following puzzle area seemed bugged in a couple ways... The wall south of the first lever and wall opposite it could just be walked through (I only tried AFTER flipping the lever, wasn't sure if it was always that way). There was a destructible wall near a leaking pipe I was able to see but simply could not punch nor shoot, no matter where I tried. Eventually I found I could grab a fuse through the northernmost room by clicking over a wall from the hanging gear room, but it still couldn't help me beat the room, even out of sequence. :(