"Broke up a pair, did he.....hope he brought extras."
The answer to your question is found in Genesis 7:1-2 (Emphasis added):
1. Then the LORD said to Noah, “Enter the ark, you and all your household, for you alone I have seen to be righteous before Me in this time.
2. “You shall take with you of every CLEAN ANIMAL BY SEVENS, a male and his female; and of the animals that are NOT CLEAN TWO two..."
The answer to your question is simple; Noah was instructed to take SEVEN pair of each of the animals that were denoted as "clean" into the ark and thus provision was made by God for an added number of clean animals necessary for sacrifice. So while one mating pair of animals was broken up, there was an abundant supply of "extras" as it were.
No stones... just biblically answering your question.
Plus, they were in the ark the better part of a year, so there were likely some “extras” born during that time.