Second bug was right after you break into the "bank vault" and get into the chair. Once they power you down and escort you outside when I woke up I ran and hit from the aliens. I was over in the alcove and was stealthed and backing up while crouching. I fell through the world. I fell for about 30-40 seconds then the game thought I completed that level and took me to the next one. I completely missed that level and all the action and Alien Goop I could have gotten =(. Anyone have this (probably very rare) problem of falling through the world and missing out on a level?
Maybe when I get home I will load up some screen shots of the tracers.