What does "in-" mean in the english language?

I've always thought the same thing! GREAT question! I hate the words "ingenius" and another one is "invaluable" which both have positive meanings -but I have to actually think about the meanings before I use them or when I hear them (and I'm a native English speaker :X hahaha) because to me they always sound the opposite like in "insincere"

Ingenius doesn't not exist! It's either "Ingenious" or "Ingenuous".

Ingenious or Ingenuous & Insincere are from Latin, but the -in prefixes of all the words have different meanings due to how words were combined.

in-
a prefix of Latin origin, corresponding to English un-, having a negative or privative force, freely used as an English formative, esp. of adjectives and their derivatives and of nouns (inattention; indefensible; inexpensive; inorganic; invariable). It assumes the same phonetic phases as in-2 (impartial; immeasurable; illiterate; irregular, etc.). In French, it became en- and thus occurs unfelt in such words as enemy (French ennemi, Latin inimicus, lit., not friendly).

the reason that word prefixes are different from the various suffixes, is because they all have different etymologies. which is why english is one of the most difficult languages to learn.
there are different ways to define the prefix "in-", which also makes differentiating word more difficult. 'in-' could mean, not, non, or un-. but it could also mean, in, within, or into.