i'm not sure why I've never pondered this before but now that i have i find myself curious how others handle it.
So you have a dungeon and at the entrance is an average encounter, beyond the entrance is a cavern containing a challenging encounter. while the PC's engage the creatures at the entrance the monster in the cavern is alerted and joins the battle. Obviously if its a tribe the Pc's could easily find themselves overwhelmed and the AVG encounter soon becomes a fight for survival. how do some people handle this? do you place the CR's in a curtain area and what happens is the players problem, adjust for it by planning a max CR over a curtain area, make your areas static and ignore common sense? Usually i just build CR's by area and if they join or merge well the players probably created the situation and now must handle it. But is this really the right way to handle it? A tribe for instance, a party could find itself easily facing an ECL of +5, +10, +15 or even higher. putting players against such an ECL just seems wrong in so many ways....
You could always give them goodies to use in the dungeon. I'm sure they'd have no problem with that!