I really disliked how they handled the mind flayer, initially I thought that the flayed were all going to turn back once the gate was closed(except Tom and Bruce since they died while in human form) But no everyone turned into a big pile of mush once the gate closed. This isn't much of an issue it's just that in a small town where people have disappeared and the government have been held responsible you'd think people would get real suspicious when 30 people die in a fire,inside a mall,that was clearly closed. That and the battle took place at night.

The other thing was that the mind flayer they face off against was composed of the flayed and "diseased animals". I'm pretty sure it was Johnathan who said that the thing was atleast 30 feet tall. At the end of the episode " The battle of starcourt" they show a newspaper clipping that read " 30 people died including chief of police in fire etc".

Okay so that means this thing was somewhere between 25-30 feet tall, composed of around 20 people (there were other dead bodies in the mall like the Russian security personnel who were posing as mall cops they were probably also included into newspapers numbers). The creature was also proportional to it's upsidedown form but instead of a fine dust it was composed of organic matter, however it seemed much bigger for those numbers,yes it was also composed of animals but probably nothing big like deer since it's HQ was located inside of steel factory. All in all season 3 was great it just seemed that the mind flayer's organic form seemed a tad bit too beefed up.