A litter of kittens have more than one father, and so can a litter of puppies.
In fact, any of the species that have litters and can be bred multiple times during one heat cycle can have offspring with different sires.
The scientific term for such breeding is superfecundation.
Female cats are induced ovulators and need to be bred before they release eggs from their ovaries.
In general, they are bred several times before they ovulate, so there could be sperm from different males in the reproductive tract before the eggs are released.
But having multiple sires is probably not very common.
In the wild state, one dominant male will generally breed the female, so all the kittens usually have the same father, and owners of pedigreed cats make sure that only one tomcat is allowed to mate with a queen.
Determining the sires of a litter of kittens would require paternity testing involving their DNA.