Corrected entry: After Rock and Pierce believe they've defeated Fishburne at "The Zit," they return to the third precintct in the lymph nodes. Immediately upon entering his boss's office, Rock asks Brandy a question, but he mistakenly refers to her as Brandy instead of using her character name, Leah. It's easy to notice because Rock even corrects himself in the line of dialogue; "Brandy, I mean, Leah, what are you doing here?"
Corrected entry: A little problem with Thrax's plan: viruses, bacteria, etc. don't cause fevers themselves. That's the body's response to kill the parasites.
Correction: A standard infection-caused fever is called hyperthermia - a warming of the body to kill the infection. Thrax is causing hyperpyrexia - a syndrome where the body's normal temperature auroregulation is malfunctioning, exactly what is happening in the film.
Corrected entry: Near the end when Shane gets off the bus to go to her dad, her uncle yells to the teacher "It's ok I'm her niece."
Correction: Her uncle is an idiot. If you watch it again, you'll see he looks quite confused and mutters to himself afterward.
Corrected entry: While waiting to leave the bladder, Drix says that he wasn't designed to fight a virus. Yet Drix is a cold pill. The common cold is a virus.
Corrected entry: After Frank's zit is popped, the "after-effects" (scabbing, etc.) seem to be skipped over, into normal skin again, and the healing process takes days for that to happen.
Correction: Some people and some zits don't scab as bad as others. This could be one of those that doesn't have much after effects.
While the zit scene was done as a gag, there's no sign of a previously popped zit. Even if it wasn't much, there should be something. Plus, in the body we see a hole and Jones says they're going to call for a scab.
Correction: If you look at the special features on the DVD, it shows that they improvised the whole movie. And they added in little jokes that weren't in the script, such as this one... it's clear he meant to make this "mistake".