Depends on what kind of plant or plant 'fruit' you are talking about... :/ oh I thought you said how... oops, because seeds are kinda hard to digest and swallow, they are actually full of protein and stuff but most aren't too great for you. and the stems are just to take nutrients to the plant like an umbilical chord kinda... you wouldn't want to eat an umbilical chord now would you? O.0
Of which fruit? Usually it is because the seeds and stems are indigestible. But there is NO WAY I'm taking the seeds out of strawberries, raspberries and blueberries! Also, with pomegranates, what you eat ARE the seeds.