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.
La Forge tells O'brien "another minute, and we'd both be fossils." Data replies " Not precisely Geordi, true fossilization requires several millennia." Data's statement is false. While at the time of filming, it may still have been believed so, it has been proven that fossilization can happen in a very short time. Experiments have show fossilization occurring in as short as a few hours. It depends on the right chemical conditions, not time.
O'Brien says, "The transporter has detected unidentified microbes in Commander Riker's body." In reality, any time they visited any world with any life on it, if they so much as breathed the air, they would have unidentified microbes in their bodies.
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.