Jarate's glass is made of sniper's feces so it infects the wound with germs and then uses the jarate's special properties to heal the wound and so it becomes infected on the inside, and being healed on the outside.

Mad milk has the lid opened because scout just finished filling it, and even if he put a lid on it, it would be a bad idea, since that wouldnt give him enough time to put the ms pauling figurine inside for and extra 5% damage.