Put a filter sponge over the intake of the siphon hose.
For cleaning the bottom of fry tanks I use a length of air line zip tied to a dowel rod, into a bucket. Wipe the bottom with a paper towel first, let it settle, siphon the debris. Shining a light on one side of the tank will either draw fry to or away from the light, move the fry away from where you are working. You'll always end up with a few in the bucket, suck them up with a turkey baster, squirt them back in the tank.