Soy is simply a filler. Much like corn or wheat. In some cases these ingredients can cause allergic reactions (diarrhoea or vomiting), but generally they are simply a "nothing" ingredient used to help fill the pup's stomach and reduce the cost of producing for the manufacturer.
Try to look for foods which do not use soy. Rice is the best alternative as a "filler" since it is an excellent protein and carb source as well as a method for curbing your pup's hunger.