Maybe we should just read the novel to understand it better, the summary just summarize things without giving us any opportunity to understand things by ourself...They could've easily fixed the Gilver stuff by saying that he was an imperfect clone or something.
Another one is where it says Mundus didn't have complete control over Vergil when he converted him until he gave him his amulet back then he completely obeyed. Makes no sense because upon seeing Dante's amulet, he freaks out and would later painfully remove his mask/helmet thing.
If they ever relese it in English