Only if they are really hard or rubbery .... good point, though: If they're still intact, then they haven't travelled thru a filter turbine. They'd be shredded. Great topic...
Next question: Is the poop real heavy? I.e. do you see it swirled up to higher water reagions so that it actually gets sucked into the filter, or does it (mostly) fall out of the fish's ass and drop to the ground and stay there like a rock? Also, is your outlet to the filter near the bottom or somewhat off the ground? If it's too high and the poop is "heavy", then you may have to extend the outflow to reach the bottom, e.g. by adding a piece of rubber hose.