Your fry should be separated from other fish or mature guppies.
Any food fed should be powdered or fine so that the fry can eat it. If feeding flakes feed the fry several times instead of lot at once cause fry won’t eat the water softened flake and this would cause water clouding. Occasionally try feeding the fry with spinach leaves and pealed pea pods.
Good aerated conditions promote growth and voids diseases away helping to have maximum number of surviving fry.
Strong flow or suction can destroy the fins of fry and in extreme cases lead to their death. Using a filter for fry tank is not very necessary. Fry will do well without it.
Scoop out water slowly and make sure you’re not taking out any fry before dumping the water.
If the water problem persists, visit your nearest pet shop and get water test kits to maintain water quality.
Diseased fry have a very low chance of surviving. Remove any sick fry immediately. Do not medicate a tank with fry in it, as it is too difficult for a regular fish keeper to use the right dosage instead destroy it though it may sound cruel.