There are two theories. One; the fish will only grow as big as the tank allows, so if the tank is small, say under 5 gal US then the fry won't have enough room to grow and will be stunted.
Two; fry give off hormones (All fish do) but fry give off a hormone that, when it gets to a sufficient concentration in a tank the fry will stop growing, because these hormones indicate that the environment can not support a fish of a larger size.
A third, now that I think of it, is inbreeding or genetic problems, if the mother was small, her fry may be smaller.
Just some suggestions.
How big is the tank you have the fry in? How big is the guppy tank? How often do you do water changes, and what volume? Do you have a test kit or happen to know your water parameters?