Upon further testing, I have found that sometimes the game 'forgets' what type of Beast the child of a pregnant character should be, if you reload a save containing pregnant characters.
Reloading sometimes solves the issue. Currently, I believe the issue may be due to how the game interprets or decides what Beast subtype a character is supposed to be, which I believe explains why loading a save and minotaur enemies may produce inconsistent end results on a pregnancy.