When you say "encounter," what do you mean? The general parlance is an encounter starts when you roll initiative, and ends when the party is no longer in imminent danger (3 or 4 rounds later, in most cases). The classic dungeon where the characters are exploring hostile territory will feature several or even many encounters, depending on how big it is and what lives there. They may or may be able to get a rest in, depending on just how hostile the dungeon is or how much time pressure they are under.

It sounds like...you want to incorporate MORE short rests into your game, but don't know where to put them? Is that correct?