If you are seeing sesame seed type things, then I would have to suspect tapeworms. Fly eggs are small, white, and about the size of this apostrophe: ' . So, if you are seeing larger things you suspect are eggs, and they look like dark sesame seeds, these are probably dried up tapeworms.
However, if your cat and kittens are not clean, you can certainly get a maggot problem if there are flies around!!! THis is very dangerous to the kittens! Are you just finding these in the litter box?
One thing you can do is collect some of these things you suspect to be maggots in a baggie, and some of the eggs, and take them to a vet office. They can tell you if you have a tapeworm problem or a maggot/fly problem. We do this for free, but some vets do charge for an ID of a parasite. If there are tapeworms, your vet can dispense a medication to kill the worms. It will pass into the milk, but should not harm the kittens.
If you have a maggot problem, you need to examine all the kittens and your cat, and make sure they are all very clean. Give momma cat a good bath if needed to remove any afterbirth. Rinse her well so no soap is on her nipples. Change bedding once or twice daily. Keep the litter box scooped immediately. If you notice any maggots in the skin of your cat or kittens, this requires immediate vet attention.
Please reply if you have further questions.