Dr Pulaski keeps talking about bringing the "growth rate" down and when she does, she stops or shows down "treatment". The pathogen is still present even when the growth rate is 0% - treatment must continue at the same aggression level until the pathogen is gone else the growth rate will just go right back up.
In Star Trek: The Next Generation: The Battle, Dr. Crusher claims 24th-century science "...has mapped the brain." But despite this, Dr. Pulaski doesn't understand the endorphins the brain produces under different circumstances.
Riker sees things in flashback that he couldn't possibly remember. Like scenes aboard the Enterprise while he's off ship at the time. He also sees the test sequence put to Data in Star Trek: The Next Generation: The Schizoid Man. He even sees subtitles in flashback at one point.