"I am not crying."
Is this why Pokémon sounds were translated as "cries" in the english games?
Because Japanese use the same verb for both crying and animals making noises?
Yes because the conjugation pattern here is "~て いる", and いる is what gets changed into いません.
Or maybe I did not understand the question? If the " was meant to represent a pause in speaking, then the answer would be "kinda yes, but...". I do think it is common that the い sound to be spoken softly and quickly, thus giving the appearance that there is no い. As far as what I've heard speakers in the Tokyo/Chiba area say, the い sound ,although very quiet, is still there.