"The pill you took is part of a trace program, its designed to disrupt your input output carrier signal so that we can pinpoint your location"
- Morpheus (SP?lol)
I dont think the pill is tricking the machines at all, i belive that while they have a new redpill in that extraction room there are alot of things going on you dont know about. For instance A-poc was trying to lock onto Neo's signal, and Trinity was strapping Neo in while morpheus was talking to him,but what were Switch and cypher doing with all thier gadgets?
I like to think they were hacking the program code of the matix distorting it slowly in order to make the matrix appear less real for Neo, which is why the broken mirror started to liquify and once it started climbeing up his arm he knew it couldnt be real, so thats what woke him up.
So now that he is awake 1 of 2 thing happens, either he's flushed and goes where all the bodys dead or alive go, and the HvCft is just there to scoop him up before he makes his way to the "liquify factory" (lol) via the sewers. OR perhaps the tubes he slid down have alrternate routs and maybe they they send the redpills to a diffrent area. You know close off this door and open another just change the course of the tube.
Remember the machines know about zion and every so often they go down there to destroy it. Zion is basicly kinda like a trash can, and redpills are the trash. Sooner or later you gotta take the trash out becasue it gets to full.