Ms. Albert kicks the boat motor to restart it after it stalls. Kicking a boat motor won't restart it, since the motor requires turning over to start.
Mr. Blanc runs out of ammunition in one of the cutscenes. Given that he is in Warring States Era Japan and therefore cannot find more ammunition for his pistol, he should not be able to fire it at all like he does.
In Onimusha 1 and Onimusha 2 matchlock muskets were proven to be effective against genma. This being the case, it does not make sense that a modern assault rifle like the FAMAS would be unable to do harm to the genma unless wielded by the main characters; the French police and special forces should be able to fight better.
Samanosuke talks about time as if he knows how it works, but he only just got transported in time recently and before then never had any interaction with time travel.