If you're choosing the Acolyte background, it assumes you are choosing Magic Initiate, Cleric. If you choose the Sage Background, it assumes you are doing Magic Initiate, Wizard.
If you want to override this, don't select an origin feat in the builder and instead choose it on feats section in the character builder.
Apologies if this is a repeat; I saw this formerly was a bug when in TCoE, but seems to have popped up again now in PH24.
If you're choosing the Acolyte background, it assumes you are choosing Magic Initiate, Cleric. If you choose the Sage Background, it assumes you are doing Magic Initiate, Wizard.
If you want to override this, don't select an origin feat in the builder and instead choose it on feats section in the character builder.