Baby fish, like most baby animals, can't reproduce. As far as I know, mollies reach sexual maturity at four to five months of age. As members of the livebearer family, it is sometimes difficult to tell the sex of a molly at a young age, because the male sex organs are among the last mature features to develop. After about three months, males appearing in the baby tank should be removed to prevent inbreeding (assuming that the fish were from the same mother, any resultant pregnancies will probably have a high rate of deformities.)
If you are breeding for a particular trait, you can cross a molly back with its mother. However, most serious breeders of live-bearers do most of their important breeding with virgin females. This is because mollies, along with platies, guppies and sWordtails, can store sperm from a previous mating and become pregnant and bear young five or six times from a single mating. This means that after the first mating, it is often impossible to tell who the father is. Crossing brother and sister would be easier, but again, the birth defect rate is likely to be significantly higher. Serious breeders generally cull out any fish that aren't brightly colored and perfectly formed anyway, but I would personally try to avoid inbreeding because i don't want to cull fish if I can avoid it.
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