The point here, in this bracketed (interpolated, competely irrelevant to the Iliad) passage of Eustathius, seems to be that small fish (e.g. smelt, anchovies, herring), popularly known to us as "small fry," actually fry very quickly, and are immediately edible. Such a fish was called ἀφύη because its form (φύη) was so ugly as to appear "formless" or "shapeless" (ἀ + φύη). Apparently, however, its taste was good enough, and it was small enough to fry so quickly that it seemed to be cooked almost as soon as it saw the fire under the frying pan. So εἶδε πῦρ ἀφύη (literally, "the small fry has seen the fire") came to mean something like "It'll be done in a heartbeat."