Factual error: In the scene where the FBI agents have taken Giovanni Ribisi in for interrogation, one of the FBI agents says at one point "...and I want the whole C:/ Drive backed up on a floppy.", which is pretty hard to do, if not impossible, unless you've got about a 5Mb hard disk drive (depending on compression levels). But later on in the scene where Ribisi is actually doing it, he does it in about 10 seconds...with a 1.44MB floppy.
Other mistake: In the scenes after Giovanni Ribisi is arrested, his looks are constantly changing. In scenes where he is talking to Vin Disel his face is very fat. When he walks by Abby's desk he is thin again. If you get Boiler Room on DVD you'll see an original ending where Ribisi is thin all the way through the end of the movie; Because Giovanni was preparing for a film that required him to gain 30 something pounds, the scenes that needed to be reshot for a different ending are very defined.