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You're more than likely breeding it with a Ditto. Anything bred with Ditto doesn't pass ball down and just goes in a normal PokeBall.
Actually that's not true, I breed constantly and had a female Audino in a Heal ball that I bred with a Ditto and it passed down. In fact, there were several instances over the past few days I needed to breed two lines of pokemon (one with the egg moves, one with the ability I wanted) until I got a male in a regular pokeball just so that I DIDN'T get the ball the mother was in. Males bred with Ditto can't pass down the pokeball that's true, but "anything" bred with ditto CAN in fact pass it down if that "anything" is female:
https://www.gamefaqs.com/boards/696959-pokemon-x/67710644
https://www.neoseeker.com/forums/60943/t1913151-ditto-breeding-which-pokeball/
https://gaming.stackexchange.com/qu...ls-passed-down-from-the-parents-when-breeding