The people who wrote the books are human, therefore, there are bound to be mistakes. Plus, S-IIIs were secret, anything they find would be untold to even other parts of the military (modern examples would be the armour the M1A2 Abrams uses, no one knows what it's made of besides the tankers and the people who make the vehicle). For 4 books, those are the only examples you found that show problems? That's fantastic. I'm surprised you didn't find more(not saying you didn't...). I would even say those are not problems, remember the book still has to appeal to a general audience, not just people who like Halo for what it is. So him facing an Elite should be explained as best as possible, even though it seems weird, it's probably the best way to show it. Cortana seeming to know the language, would you like the writer to explain the logic Cortana used to figure out the language? That would be boring. I think the books are as good as they're going to be.
"Killing Solves All Problems - No Man, No Problem" - Josef Stalin