The gods of the realms have alliances and enemies just like any kind of powerful faction would. For example, Loviatar is allied with Bane, possibly neutral with Shar and Bhaal, but opposed to Ilmater, Eldath and Lliira.
So a worshiper of Bane might gladly take a boon from Loviatar, but a worshiper of those opposed gods would not, because it would be accepting a boon from a god directly opposed to them. If you were a cleric of those gods and you accepted a boon from Loviatar, your clerical powers might be reduced or even withdrawn (at least, in tabletop, not in BG3).
