usage of the "in" prefix

You're making an assumption about derivation which is not warranted. Ingrate, meaning someone who is not thankful, derives directly from a Latin word, through French. Ingratiate derives, through Italian, from an entirely different Latin word. The in- prefix can have two different meanings, one meaning "not," the other meaning from, or upon, or out of. Words such as inherent or inhabit are formed using the second sense of in-. But that doesn't apply here because these two words derive from different words in Latin, which, although the Latin words have their roots in the same word, had different meanings before they entered English.