It is worth noting that CR is a suggestion, not a rule. DMs can and do modify encounters to better fit the story they want to tell and the party they are running all the time.
Additionally, DnD is balanced around the idea that if you lose a fight you're just... Dead. Campaign over outside DM being generous with a means of returning to life. In Baldur's Gate we have the luxury of taking on higher difficulty fights without that being a concern, so CR as defined on the tabletop won't necessarily translate to "never, ever attempt this fight" in Baldur's Gate because we have the luxury of reloading if things go terribly wrong and trying again.
Video game balance and tabletop balance are quire different. And as for lore, our primary enemies in Act 1 are imps, humans, gnolls, and goblins. Also, after looking it up real fast:
Green hags, phase spiders, and minotaurs ae CR 3. Completely acceptable for when we meet them in the game.
So there's really not much in the game we're fighting right now that is dramatically beyond our party's ability to handle.