"The girl eats a lemon" -- "a lemon" indicates that there is one whole lemon.
"The girl eats lemon" -- no determiner before the singular noun "lemon" means that it is not being used in a countable way, but as a mass noun, so the girl is eating an unspecified quantity of the substance "lemon".
μία is used for feminine nouns, ένα is used for neuter nouns.
λεμόνι is neuter - as are all(?) nouns that end in -ι.
Usually, you can tell the gender of a noun from the ending, though some endings can be on nouns from more than one gender (particularly -ος, which is most often masculine but not always).