The Divine Maiden collapsed on a hill. Later, she is found all the way on the bottom of the hill with no way of having gotten there.
Certain grammatical mistakes are present, such as always calling the 'GUARDIANS' force by plural.
Some grammar mistakes are present, such as a character saying '...a Relics...' instead of '...Relics...' or '...a Relic...'.
Karen explains about the security gates as if the team hadn't encountered them before. However, by the time she does explain about the security gates, the team will have to have gone through a number of them to get to that location.
If the Player does not charge the photon energy, a weapon will stay empty until drawn, even though it recharges when drawn and there is enough time for it to have fully recharged.
Even if one faction were threatened by something, there would be no need to call for a galaxy-wide state-of-emergency simply because galaxies are so vast that the likelihood of something happening in multiple spots at the same time is very low.
Destroying SEED cores should not be enough to stop an infection, since there are still sores around.
The cars on the train in Chapter 4 are almost completely empty in spite of the train being a cargo train.
Musashi says that the team interfered on the train, when the team was assigned there to begin with.
Karen says that the rogues kidnapped people from the train. Other than the team, there was no one else on the train.
Magashi is given 4 A-photon reactors and refers to them in the singular.