crazy, and a bit nasty @_@ yeah my dumb brother left it in his room I think for a while i'm guessing, who knows what was inside the glass, but he recently cleaned his room so yeah @_0 eww. Should I be worried about his health though in his room if they eat decaying stuff and they seemed to have breed in his room, since there were so many on the glass, or was it just because of the glasses contents?

I would be concerned about what kind of bacteria are making the contents of the glass palatable to the flies, though. The health threat from flies, cockroaches is generally inflated by the media. One should not dismiss the possible contamination, but if a person is generally in good health, then their immune system can usually fend-off germs.

wow really, crazy, so will they hatch then u think soon?

I would suggest putting the jar in a large, clear plastic bag allowing a small amount of air to enter, but not too much to allow whatever emerges from escaping. When adult forms emerge, take a few digitals and submit these images. We should be able to ID them then.

Well i think their dead, cause i sprayed them and they didn't move, or unless their just waiting to hatch. I took it outside though, parents didn't want it inside @_@ so hopefully they'll be ok outside.

The pupae are an inactive stage between the larva and the adult fly--like a butterfly chrysalis--so they wouldn't be able to move if they are alive... I'm sure they'll be okay outside.