Most filters should have a sort of cage over the intake that will prevent fish from being sucked in. If it's missing, cover the intake with a bit if old pant hose rubber-banded to the intake tube and order a replacement from the filter's manufacturer.
If your fish are too small to be screened out by this cover, you can add a piece of panty hose over the cover itself until they're grown or even permanently if you rinse it sometimes.
Fish being stuck to the intake cage is usually a sign that it's about to die, in which case you have bigger problems than it being stuck. See the Disease Section http://www.petfish.net/kb/12/
I have seen some cases where seemingly perfectly healthy fish are mysteriously sucked to the filter and killed. The best course of action in this case is to buy a new filter, most of the large name-brands like aqua clear, marineland, and whisper are reputable and reliable.