Naomi says her grandfather was in the FBI, but later, Master Miller mentions "her grandfather" and "her father" when talking about him.
If Snake gets a cold after escaping from the prison cell and calls Naomi, Snake will ask if Naomi can do something to cure it. Naomi replies that the nanomachines in Snake's blood don't carry antibiotics. The common cold is a virus, and antibiotics would be ineffective against it. Antibiotics work against bacterial infections.
When Naomi calls Snake and says "Campbell and the others are busy right now, I'm using a different codec". The player's codec reports that she's calling from the same frequency. However this still makes sense: it's possible to have several radio handsets using the same frequency.
After Snake calls Meryl to tell her that he rescued Otacon, Otacon says that he could hear music. This shouldn't be possible because, as Campbell explained, the nanomachines stimulate the small bones in Snake's ear; no one but him should've been able to hear it.
Naomi refers to Dr. Clark as a man. However, Clark is a woman.
Liquid's monologue on genetic engineering is scientifically comprehensible, however the technical terminology is misused. For example, when discussing phenotypes, it would be correct to discuss dominant and recessive traits, rather than dominant and recessive genes as Liquid does. "Analogue cloning" and "digital cloning" are not real scientific terms, however this is excusable given the game's science-fictional setting.